Acta crystallographica. Section D, Biological crystallography最新文献

筛选
英文 中文
Structural basis of Deerpox virus-mediated inhibition of apoptosis. 鹿痘病毒介导的细胞凋亡抑制的结构基础。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-08-01 Epub Date: 2015-07-28 DOI: 10.1107/S1399004715009402
Denis R Burton, Sofia Caria, Bevan Marshall, Michele Barry, Marc Kvansakul
{"title":"Structural basis of Deerpox virus-mediated inhibition of apoptosis.","authors":"Denis R Burton,&nbsp;Sofia Caria,&nbsp;Bevan Marshall,&nbsp;Michele Barry,&nbsp;Marc Kvansakul","doi":"10.1107/S1399004715009402","DOIUrl":"https://doi.org/10.1107/S1399004715009402","url":null,"abstract":"<p><p>Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that the Deerpox virus inhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteins via two conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 8","pages":"1593-603"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715009402","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33967495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 24
An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase. P460辅因子在羟胺氧化还原酶中的意外反应性。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-08-01 Epub Date: 2015-07-31 DOI: 10.1107/S1399004715010706
Andreas Dietl, Wouter Maalcke, Thomas R M Barends
{"title":"An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase.","authors":"Andreas Dietl,&nbsp;Wouter Maalcke,&nbsp;Thomas R M Barends","doi":"10.1107/S1399004715010706","DOIUrl":"https://doi.org/10.1107/S1399004715010706","url":null,"abstract":"<p><p>Hydroxylamine oxidoreductases (HAOs) contain a unique haem cofactor called P460 that consists of a profoundly ruffled c-type haem with two covalent bonds between the haem porphyrin and a conserved tyrosine. This cofactor is exceptional in that it abstracts electrons from a ligand bound to the haem iron, whereas other haems involved in redox chemistry usually inject electrons into their ligands. The effects of the tyrosine cross-links and of the haem ruffling on the chemistry of this cofactor have been investigated theoretically but are not yet clear. A new crystal structure of an HAO from Candidatus Kuenenia stuttgartiensis, a model organism for anaerobic ammonium oxidation, now shows that its P460 cofactor has yet another unexpected reactivity: when ethylene glycol was used as a cryoprotectant, the 1.8 Å resolution electron-density maps showed additional density which could be interpreted as an ethylene glycol molecule covalently bound to the C16 atom of the haem ring, opposite the covalent links to the conserved tyrosine. Possible causes for this unexpected reactivity are discussed.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 8","pages":"1708-13"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715010706","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33899169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate. 医源性病原体鲍曼不动杆菌体内必需代谢酶莽草酸激酶与莽草酸复合物的结构。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-08-01 Epub Date: 2015-07-31 DOI: 10.1107/S139900471501189X
Kristin A Sutton, Jennifer Breen, Ulrike MacDonald, Janet M Beanan, Ruth Olson, Thomas A Russo, L Wayne Schultz, Timothy C Umland
{"title":"Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate.","authors":"Kristin A Sutton,&nbsp;Jennifer Breen,&nbsp;Ulrike MacDonald,&nbsp;Janet M Beanan,&nbsp;Ruth Olson,&nbsp;Thomas A Russo,&nbsp;L Wayne Schultz,&nbsp;Timothy C Umland","doi":"10.1107/S139900471501189X","DOIUrl":"https://doi.org/10.1107/S139900471501189X","url":null,"abstract":"<p><p>Acinetobacter baumannii is an opportunistic Gram-negative pathogen that is an important cause of healthcare-associated infections exhibiting high mortality rates. Clinical isolates of multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. baumannii strains are increasingly being observed. Compounding this concern is the dearth of new antibacterial agents in late-stage development that are effective against MDR and XDR A. baumannii. As part of an effort to address these concerns, two genes (aroA and aroC) of the shikimate pathway have previously been determined to be essential for the growth and survival of A. baumannii during host infection (i.e. to be essential in vivo). This study expands upon these results by demonstrating that the A. baumannii aroK gene, encoding shikimate kinase (SK), is also essential in vivo in a rat soft-tissue infection model. The crystal structure of A. baumannii SK in complex with the substrate shikimate and a sulfate ion that mimics the binding interactions expected for the β-phosphate of ATP was then determined to 1.91 Å resolution and the enzyme kinetics were characterized. The flexible shikimate-binding domain and LID region are compared with the analogous regions in other SK crystal structures. The impact of structural differences and sequence divergence between SKs from pathogenic bacteria that may influence antibiotic-development efforts is discussed.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 8","pages":"1736-44"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S139900471501189X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33899172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Structural evidence for asymmetric ligand binding to transthyretin. 不对称配体与转甲状腺素结合的结构证据。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-08-01 Epub Date: 2015-07-28 DOI: 10.1107/S1399004715010585
Michele Cianci, Claudia Folli, Francesco Zonta, Paola Florio, Rodolfo Berni, Giuseppe Zanotti
{"title":"Structural evidence for asymmetric ligand binding to transthyretin.","authors":"Michele Cianci,&nbsp;Claudia Folli,&nbsp;Francesco Zonta,&nbsp;Paola Florio,&nbsp;Rodolfo Berni,&nbsp;Giuseppe Zanotti","doi":"10.1107/S1399004715010585","DOIUrl":"https://doi.org/10.1107/S1399004715010585","url":null,"abstract":"<p><p>Human transthyretin (TTR) represents a notable example of an amyloidogenic protein, and several compounds that are able to stabilize its native state have been proposed as effective drugs in the therapy of TTR amyloidosis. The two thyroxine (T4) binding sites present in the TTR tetramer display negative binding cooperativity. Here, structures of TTR in complex with three natural polyphenols (pterostilbene, quercetin and apigenin) have been determined, in which this asymmetry manifests itself as the presence of a main binding site with clear ligand occupancy and related electron density and a second minor site with a much lower ligand occupancy. The results of an analysis of the structural differences between the two binding sites are consistent with such a binding asymmetry. The different ability of TTR ligands to saturate the two T4 binding sites of the tetrameric protein can be ascribed to the different affinity of ligands for the weaker binding site. In comparison, the high-affinity ligand tafamidis, co-crystallized under the same experimental conditions, was able to fully saturate the two T4 binding sites. This asymmetry is characterized by the presence of small but significant differences in the conformation of the cavity of the two binding sites. Molecular-dynamics simulations suggest the presence of even larger differences in solution. Competition binding assays carried out in solution revealed the presence of a preferential binding site in TTR for the polyphenols pterostilbene and quercetin that was different from the preferential binding site for T4. The TTR binding asymmetry could possibly be exploited for the therapy of TTR amyloidosis by using a cocktail of two drugs, each of which exhibits preferential binding for a distinct binding site, thus favouring saturation of the tetrameric protein and consequently its stabilization. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 8","pages":"1582-92"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715010585","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33967494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 23
Detection of trans-cis flips and peptide-plane flips in protein structures. 检测蛋白质结构中的反式顺式翻转和肽平面翻转。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-08-01 Epub Date: 2015-07-28 DOI: 10.1107/S1399004715008263
Wouter G Touw, Robbie P Joosten, Gert Vriend
{"title":"Detection of trans-cis flips and peptide-plane flips in protein structures.","authors":"Wouter G Touw, Robbie P Joosten, Gert Vriend","doi":"10.1107/S1399004715008263","DOIUrl":"10.1107/S1399004715008263","url":null,"abstract":"<p><p>A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans-cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans-cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure-function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT_CHECK. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 8","pages":"1604-14"},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33967496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure of protease-cleaved Escherichia coli α-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment. 蛋白酶裂解的大肠杆菌α-2-巨球蛋白的结构揭示了蛋白酶夹持构象激活的推定机制。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715008548
Cameron D Fyfe, Rhys Grinter, Inokentijs Josts, Khedidja Mosbahi, Aleksander W Roszak, Richard J Cogdell, Daniel M Wall, Richard J S Burchmore, Olwyn Byron, Daniel Walker
{"title":"Structure of protease-cleaved Escherichia coli α-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment.","authors":"Cameron D Fyfe, Rhys Grinter, Inokentijs Josts, Khedidja Mosbahi, Aleksander W Roszak, Richard J Cogdell, Daniel M Wall, Richard J S Burchmore, Olwyn Byron, Daniel Walker","doi":"10.1107/S1399004715008548","DOIUrl":"10.1107/S1399004715008548","url":null,"abstract":"<p><p>Bacterial α-2-macroglobulins have been suggested to function in defence as broad-spectrum inhibitors of host proteases that breach the outer membrane. Here, the X-ray structure of protease-cleaved Escherichia coli α-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition. In this competitive mechanism, protease cleavage of the bait-region domain results in the untethering of an intrinsically disordered region of this domain which disrupts native interdomain interactions that maintain E. coli α-2-macroglobulin in the inactivated form. The resulting global conformational change results in entrapment of the protease and activation of the thioester bond that covalently links to the attacking protease. Owing to the similarity in structure and domain architecture of Escherichia coli α-2-macroglobulin and human α-2-macroglobulin, this protease-activation mechanism is likely to operate across the diverse members of this group. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1478-86"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34262927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein. 控制晶体脱水触发空间群开关并形成巨细胞病毒即早1 (IE1)蛋白的三级结构。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715008792
Stefan Klingl, Myriam Scherer, Thomas Stamminger, Yves A Muller
{"title":"Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein.","authors":"Stefan Klingl,&nbsp;Myriam Scherer,&nbsp;Thomas Stamminger,&nbsp;Yves A Muller","doi":"10.1107/S1399004715008792","DOIUrl":"https://doi.org/10.1107/S1399004715008792","url":null,"abstract":"<p><p>Cytomegalovirus immediate-early 1 (IE1) protein is a key viral effector protein that reprograms host cells. Controlled dehydration experiments with IE1 crystals not only extended their diffraction limit from 2.85 to 2.3 Å resolution but also triggered a monoclinic to tetragonal space-group transition with only minor alterations in the unit-cell parameters. An analysis of the pre-dehydration and post-dehydration crystal structures shows how dehydration rearranges the packing of IE1 molecules to meet the unit-cell constraints of the higher lattice symmetry. The transition from P21 to P43 reduces the number of copies in the asymmetric unit from four to two, and molecules previously related by noncrystallographic symmetry merge into identical crystallographic copies in the tetragonal space group. At the same time, dehydration considerably alters the tertiary structure of one of the two remaining IE1 chains in the asymmetric unit. It appears that this conformational switch is required to compensate for a transition that is assumed to be unfavourable, namely from a highly preferred to a rarely observed space group. At the same time, the dehydration-triggered molecular reshaping could reveal an inherent molecular flexibility that possibly informs on the biological function of IE1, namely on its binding to target proteins from the host cell. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1493-504"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715008792","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34262929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
From bacterial to human dihydrouridine synthase: automated structure determination. 从细菌到人二氢吡啶合成酶:自动结构测定。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715009220
Fiona Whelan, Huw T Jenkins, Samuel C Griffiths, Robert T Byrne, Eleanor J Dodson, Alfred A Antson
{"title":"From bacterial to human dihydrouridine synthase: automated structure determination.","authors":"Fiona Whelan, Huw T Jenkins, Samuel C Griffiths, Robert T Byrne, Eleanor J Dodson, Alfred A Antson","doi":"10.1107/S1399004715009220","DOIUrl":"10.1107/S1399004715009220","url":null,"abstract":"<p><p>The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1-340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr_rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain-domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 7","pages":"1564-71"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715009220","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10123611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli. 大肠杆菌半乳糖醇-1-磷酸5-脱氢酶对半乳糖醇1-磷酸的对映选择性氧化。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715009281
Rocío Benavente, María Esteban-Torres, Gert-Wieland Kohring, Álvaro Cortés-Cabrera, Pedro A Sánchez-Murcia, Federico Gago, Iván Acebrón, Blanca de las Rivas, Rosario Muñoz, José M Mancheño
{"title":"Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli.","authors":"Rocío Benavente,&nbsp;María Esteban-Torres,&nbsp;Gert-Wieland Kohring,&nbsp;Álvaro Cortés-Cabrera,&nbsp;Pedro A Sánchez-Murcia,&nbsp;Federico Gago,&nbsp;Iván Acebrón,&nbsp;Blanca de las Rivas,&nbsp;Rosario Muñoz,&nbsp;José M Mancheño","doi":"10.1107/S1399004715009281","DOIUrl":"https://doi.org/10.1107/S1399004715009281","url":null,"abstract":"<p><p>Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that belongs to the medium-chain dehydrogenase/reductase (MDR) superfamily. It catalyses the Zn(2+)- and NAD(+)-dependent stereoselective dehydrogenation of L-galactitol 1-phosphate to D-tagatose 6-phosphate. Here, three crystal structures of GPDH from Escherichia coli are reported: that of the open state of GPDH with Zn(2+) in the catalytic site and those of the closed state in complex with the polyols Tris and glycerol, respectively. The closed state of GPDH reveals no bound cofactor, which is at variance with the conformational transition of the prototypical mammalian liver alcohol dehydrogenase. The main intersubunit-contacting interface within the GPDH homodimer presents a large internal cavity that probably facilitates the relative movement between the subunits. The substrate analogue glycerol bound within the active site partially mimics the catalytically relevant backbone of galactitol 1-phosphate. The glycerol binding mode reveals, for the first time in the polyol dehydrogenases, a pentacoordinated zinc ion in complex with a polyol and also a strong hydrogen bond between the primary hydroxyl group and the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1540-54"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715009281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33981721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution). 利用IPCAS(迭代蛋白质晶体结构自动解决方案)完成蛋白质复合体结构。
Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715008597
Weizhe Zhang, Hongmin Zhang, Tao Zhang, Haifu Fan, Quan Hao
{"title":"Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution).","authors":"Weizhe Zhang,&nbsp;Hongmin Zhang,&nbsp;Tao Zhang,&nbsp;Haifu Fan,&nbsp;Quan Hao","doi":"10.1107/S1399004715008597","DOIUrl":"https://doi.org/10.1107/S1399004715008597","url":null,"abstract":"<p><p>Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1487-92"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715008597","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34262928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信