Acta Crystallographica. Section D, Structural Biology最新文献

The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-12-01 Epub Date: 2024-11-28 DOI: 10.1107/S205979832401132X

Nicholas Bragagnolo, Gerald F Audette

{"title":"The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1.","authors":"Nicholas Bragagnolo, Gerald F Audette","doi":"10.1107/S205979832401132X","DOIUrl":"10.1107/S205979832401132X","url":null,"abstract":"The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa. Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α-β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α-β loop and the D-loop prevent in vitro polymerization.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"834-849"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11626772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Photosystem II: light-dependent oscillation of ligand composition at its active site.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-12-01 Epub Date: 2024-11-28 DOI: 10.1107/S2059798324011392

Jimin Wang

{"title":"Photosystem II: light-dependent oscillation of ligand composition at its active site.","authors":"Jimin Wang","doi":"10.1107/S2059798324011392","DOIUrl":"10.1107/S2059798324011392","url":null,"abstract":"Recently, the conclusions drawn from crystallographic data about the number of oxygen ligands associated with the CaMn4 cofactor in the oxygen-evolving center (OEC) of Thermosynechococcus vulcanus photosystem II (PSII) have been called into question. Here, using OEC-omit, metal ion-omit and ligand-omit electron-density maps, it is shown that the number of oxygen ligands ranges from three in the functional OEC of monomer B following dark adaption (0F), i.e. in its ground state (PDB entry 6jlj/0F and PDB entry 6jlm/0F), to five for both monomers of PSII in photo-advanced states following exposure to one and two flashes of light. For a significant fraction of the 0F OECs in monomer A, the number is four (PDB entry 6jlj/0F). Following one flash it increases to five (PDB entry 6jlk/1F), where it remains after a second flash (PDB entry 6jlj/2F). Following a third flash (3F), it decreases to three (PDB entry 6jlp/3F), suggesting that an O2 molecule has been produced. These observations suggest a mechanism for the reaction that transforms the O atoms of the water molecules bound at the O3 and O1 sites of the OEC into O2.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"850-861"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improving macromolecular structure refinement with metal-coordination restraints.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-12-01 Epub Date: 2024-12-03 DOI: 10.1107/S2059798324011458

Kaveh H Babai, Fei Long, Martin Malý, Keitaro Yamashita, Garib N Murshudov

{"title":"Improving macromolecular structure refinement with metal-coordination restraints.","authors":"Kaveh H Babai, Fei Long, Martin Malý, Keitaro Yamashita, Garib N Murshudov","doi":"10.1107/S2059798324011458","DOIUrl":"10.1107/S2059798324011458","url":null,"abstract":"Metals are essential components for the structure and function of many proteins. However, accurate modelling of their coordination environments remains a challenge due to the complexity and diversity of metal-coordination geometries. To address this, a method is presented for extracting and analysing coordination information, including bond lengths and angles, from the Crystallography Open Database. By using these data, comprehensive descriptions of metal-containing components are generated. A stereochemical information generator for a particular component within a specific macromolecule leverages an example PDB/mmCIF file containing the component to account for the actual surrounding environment. A matching process has been developed and implemented to align the derived metal structures with idealized coordinates from a coordination geometry library. Additionally, various strategies, depending on the quality of the matches, were employed to compile distance and angle statistics for the refinement of macromolecular structures. The developed methods were implemented in a new program, MetalCoord, that classifies and utilizes the metal-coordination geometry. The effectiveness of the developed algorithms was tested using metal-containing components from the PDB. As a result, metal-containing components from the CCP4 monomer library have been updated. The updated monomer dictionaries, in concert with the derived restraints, can be used in most structural biology computations, including macromolecular crystallography, single-particle cryo-EM and even molecular mechanics.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"821-833"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11626771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Peter Main (1939-2024).

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-12-01 Epub Date: 2024-11-29 DOI: 10.1107/S2059798324010854

Eleanor Dodson, Kathryn Cowtan

引用次数: 0

Everyone is using biological structures, but how does one find the structure(s) one wants?

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-12-01 Epub Date: 2024-12-05 DOI: 10.1107/S2059798324007848

Charles S Bond, Joel L Sussman

引用次数: 0

The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era. 分子置换中经过处理的预测模型的成功率：对 AlphaFold 时代实验分期的影响。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-11-01 Epub Date: 2024-10-03 DOI: 10.1107/S2059798324009380

Ronan M Keegan, Adam J Simpkin, Daniel J Rigden

{"title":"The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.","authors":"Ronan M Keegan, Adam J Simpkin, Daniel J Rigden","doi":"10.1107/S2059798324009380","DOIUrl":"10.1107/S2059798324009380","url":null,"abstract":"The availability of highly accurate protein structure predictions from AlphaFold2 (AF2) and similar tools has hugely expanded the applicability of molecular replacement (MR) for crystal structure solution. Many structures can be solved routinely using raw models, structures processed to remove unreliable parts or models split into distinct structural units. There is therefore an open question around how many and which cases still require experimental phasing methods such as single-wavelength anomalous diffraction (SAD). Here, this question is addressed using a large set of PDB depositions that were solved by SAD. A large majority (87%) could be solved using unedited or minimally edited AF2 predictions. A further 18 (4%) yield straightforwardly to MR after splitting of the AF2 prediction using Slice'N'Dice, although different splitting methods succeeded on slightly different sets of cases. It is also found that further unique targets can be solved by alternative modelling approaches such as ESMFold (four cases), alternative MR approaches such as ARCIMBOLDO and AMPLE (two cases each), and multimeric model building with AlphaFold-Multimer or UniFold (three cases). Ultimately, only 12 cases, or 3% of the SAD-phased set, did not yield to any form of MR tested here, offering valuable hints as to the number and the characteristics of cases where experimental phasing remains essential for macromolecular structure solution.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"766-779"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11544426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Welcoming two new Co-editors. 欢迎两位新任联合编辑。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-11-01 Epub Date: 2024-11-06 DOI: 10.1107/S2059798324010350

Charles S Bond, Elspeth F Garman, Randy J Read

引用次数: 0

EMhub: a web platform for data management and on-the-fly processing in scientific facilities. EMhub：用于科学设施数据管理和即时处理的网络平台。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1107/S2059798324009471

Jose M de la Rosa-Trevin, Grigory Sharov, Stefan Fleischmann, Dustin Morado, John C Bollinger, Darcie J Miller, Daniel S Terry, Scott C Blanchard, Israel S Fernandez, Marta Carroni

{"title":"EMhub: a web platform for data management and on-the-fly processing in scientific facilities.","authors":"Jose M de la Rosa-Trevin, Grigory Sharov, Stefan Fleischmann, Dustin Morado, John C Bollinger, Darcie J Miller, Daniel S Terry, Scott C Blanchard, Israel S Fernandez, Marta Carroni","doi":"10.1107/S2059798324009471","DOIUrl":"10.1107/S2059798324009471","url":null,"abstract":"Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operations and record-keeping of a scientific facility, has been introduced. EMhub enables the easy management of user information, instruments, bookings and projects. The application was initially developed to meet the needs of a cryoEM facility, but its functionality and adaptability have proven to be broad enough to be extended to other data-generating centers. The expansion of EMHub is enabled by the modular nature of its core functionalities. The application allows external processes to be connected via a REST API, automating tasks such as folder creation, user and password generation, and the execution of real-time data-processing pipelines. EMhub has been used for several years at the Swedish National CryoEM Facility and has been installed in the CryoEM center at the Structural Biology Department at St. Jude Children's Research Hospital. A fully automated single-particle pipeline has been implemented for on-the-fly data processing and analysis. At St. Jude, the X-Ray Crystallography Center and the Single-Molecule Imaging Center have already expanded the platform to support their operational and data-management workflows.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"780-790"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11544427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural studies of β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus. 嗜热细菌钙纤维糖苷酶β-葡萄糖苷酶的结构研究。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-10-01 DOI: 10.1107/S2059798324009252

Anastasia I Sotiropoulou, Dimitris G Hatzinikolaou, Evangelia D Chrysina

{"title":"Structural studies of β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus.","authors":"Anastasia I Sotiropoulou, Dimitris G Hatzinikolaou, Evangelia D Chrysina","doi":"10.1107/S2059798324009252","DOIUrl":"10.1107/S2059798324009252","url":null,"abstract":"β-Glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus (Bgl1) has been denoted as having an attractive catalytic profile for various industrial applications. Bgl1 catalyses the final step of in the decomposition of cellulose, an unbranched glucose polymer that has attracted the attention of researchers in recent years as it is the most abundant renewable source of reduced carbon in the biosphere. With the aim of enhancing the thermostability of Bgl1 for a broad spectrum of biotechnological processes, it has been subjected to structural studies. Crystal structures of Bgl1 and its complex with glucose were determined at 1.47 and 1.95 Å resolution, respectively. Bgl1 is a member of glycosyl hydrolase family 1 (GH1 superfamily, EC 3.2.1.21) and the results showed that the 3D structure of Bgl1 follows the overall architecture of the GH1 family, with a classical (β/α)8 TIM-barrel fold. Comparisons of Bgl1 with sequence or structural homologues of β-glucosidase reveal quite similar structures but also unique structural features in Bgl1 with plausible functional roles.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"80 Pt 10","pages":"733-743"},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11448918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments. CHiMP：在蛋白质结晶显微照片上训练的深度学习工具，实现实验自动化。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-10-01 DOI: 10.1107/S2059798324009276

Oliver N F King, Karl E Levik, James Sandy, Mark Basham

{"title":"CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments.","authors":"Oliver N F King, Karl E Levik, James Sandy, Mark Basham","doi":"10.1107/S2059798324009276","DOIUrl":"10.1107/S2059798324009276","url":null,"abstract":"A group of three deep-learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The first tool, a classification network, assigns images into categories relating to experimental outcomes. The other two tools are networks that perform both object detection and instance segmentation, resulting in masks of individual crystals in the first case and masks of crystallization droplets in addition to crystals in the second case, allowing the positions and sizes of these entities to be recorded. The creation of these tools used transfer learning, where weights from a pre-trained deep-learning network were used as a starting point and repurposed by further training on a relatively small set of data. Two of the tools are now integrated at the VMXi macromolecular crystallography beamline at DLS, where they have the potential to absolve the need for any user input, both for monitoring crystallization experiments and for triggering in situ data collections. The third is being integrated into the XChem fragment-based drug-discovery screening platform, also at DLS, to allow the automatic targeting of acoustic compound dispensing into crystallization droplets.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"80 Pt 10","pages":"744-764"},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11448919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0