Acta Crystallographica. Section D, Structural Biology最新文献

Slice'N'Dice: maximizing the value of predicted models for structural biologists.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-03-01 Epub Date: 2025-02-20 DOI: 10.1107/S2059798325001251

Adam J Simpkin, Luc G Elliot, Agnel Praveen Joseph, Tom Burnley, Kyle Stevenson, Filomeno Sánchez Rodríguez, Maria Fando, Eugene Krissinel, Stuart McNicholas, Daniel J Rigden, Ronan M Keegan

{"title":"Slice'N'Dice: maximizing the value of predicted models for structural biologists.","authors":"Adam J Simpkin, Luc G Elliot, Agnel Praveen Joseph, Tom Burnley, Kyle Stevenson, Filomeno Sánchez Rodríguez, Maria Fando, Eugene Krissinel, Stuart McNicholas, Daniel J Rigden, Ronan M Keegan","doi":"10.1107/S2059798325001251","DOIUrl":"10.1107/S2059798325001251","url":null,"abstract":"With the advent of next-generation modelling methods, such as AlphaFold2, structural biologists are increasingly using predicted structures to obtain structure solutions via molecular replacement (MR) or model fitting in single-particle cryogenic sample electron microscopy (cryoEM). Differences between the domain-domain orientations represented in a predicted model and a crystal structure are often a key limitation when using predicted models. Slice'N'Dice is a software package designed to address this issue by first slicing models into distinct structural units and then automatically placing the slices using either Phaser, MOLREP or PowerFit. The slicing step can use the AlphaFold predicted aligned error (PAE) or can operate via a variety of Cα-atom-based clustering algorithms, extending the applicability to structures of any origin. The number of splits can either be selected by the user or determined automatically. Slice'N'Dice is available for both MR and automated map fitting in the CCP4 and CCP-EM software suites.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"105-121"},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456588","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

The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-03-01 Epub Date: 2025-02-28 DOI: 10.1107/S2059798325001469

Anupam Anand Ojha, Robert Blackwell, Eduardo R Cruz-Chú, Raison Dsouza, Miro A Astore, Peter Schwander, Sonya M Hanson

引用次数: 0

Expansion of the diversity of dispersin scaffolds. 扩大分散素支架的多样性。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-03-01 Epub Date: 2025-02-28 DOI: 10.1107/S205979832500110X

Alexandra Males, Olga V Moroz, Elena Blagova, Astrid Munch, Gustav H Hansen, Annette H Johansen, Lars H Østergaard, Dorotea R Segura, Alexander Eddenden, Anne V Due, Martin Gudmand, Jesper Salomon, Sebastian R Sørensen, João Paulo L Franco Cairo, Mark Nitz, Roland A Pache, Rebecca M Vejborg, Sandeep Bhosale, David J Vocadlo, Gideon J Davies, Keith S Wilson

{"title":"Expansion of the diversity of dispersin scaffolds.","authors":"Alexandra Males, Olga V Moroz, Elena Blagova, Astrid Munch, Gustav H Hansen, Annette H Johansen, Lars H Østergaard, Dorotea R Segura, Alexander Eddenden, Anne V Due, Martin Gudmand, Jesper Salomon, Sebastian R Sørensen, João Paulo L Franco Cairo, Mark Nitz, Roland A Pache, Rebecca M Vejborg, Sandeep Bhosale, David J Vocadlo, Gideon J Davies, Keith S Wilson","doi":"10.1107/S205979832500110X","DOIUrl":"10.1107/S205979832500110X","url":null,"abstract":"Microorganisms are known to secrete copious amounts of extracellular polymeric substances (EPS) that form complex matrices around the cells to shield them against external stresses, to maintain structural integrity and to influence their environment. Many microorganisms also secrete enzymes that are capable of remodelling or degrading EPS in response to various environmental cues. One key enzyme class is the poly-β-1,6-linked N-acetyl-D-glucosamine (PNAG)-degrading glycoside hydrolases, of which the canonical member is dispersin B (DspB) from CAZy family GH20. We sought to test the hypothesis that PNAG-degrading enzymes would be present across family GH20, resulting in expansion of the sequence and structural space and thus the availability of PNAGases. Phylogenetic analysis revealed that several microorganisms contain potential DspB-like enzymes. Six of these were expressed and characterized, and four crystal structures were determined (two of which were in complex with the established GH20 inhibitor 6-acetamido-6-deoxy-castanospermine and one with a bespoke disaccharide β-1,6-linked thiazoline inhibitor). One enzyme expressed rather poorly, which restricted crystal screening and did not allow activity measurements. Using synthetic PNAG oligomers and MALDI-TOF analysis, two of the five enzymes tested showed preferential endo hydrolytic activity. Their sequences, having only 26% identity to the pioneer enzyme DspB, highlight the considerable array of previously unconsidered dispersins in nature, greatly expanding the range of potential dispersin backbones available for societal application and engineering.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"130-146"},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522423","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

Human dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-03-01 Epub Date: 2025-02-26 DOI: 10.1107/S2059798325001457

Oakley Streeter, Ke Shi, Joseph Vavra, Hideki Aihara, James M Ervasti, Robert Evans, Joseph M Muretta

引用次数: 0

Has AlphaFold3 achieved success for RNA? AlphaFold3 在 RNA 方面取得了成功吗？

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-02-01 Epub Date: 2025-01-27 DOI: 10.1107/S2059798325000592

Clément Bernard, Guillaume Postic, Sahar Ghannay, Fariza Tahi

{"title":"Has AlphaFold3 achieved success for RNA?","authors":"Clément Bernard, Guillaume Postic, Sahar Ghannay, Fariza Tahi","doi":"10.1107/S2059798325000592","DOIUrl":"10.1107/S2059798325000592","url":null,"abstract":"Predicting the 3D structure of RNA is a significant challenge despite ongoing advancements in the field. Although AlphaFold has successfully addressed this problem for proteins, RNA structure prediction raises difficulties due to the fundamental differences between proteins and RNA, which hinder its direct adaptation. The latest release of AlphaFold, AlphaFold3, has broadened its scope to include multiple different molecules such as DNA, ligands and RNA. While the AlphaFold3 article discussed the results for the last CASP-RNA data set, the scope of its performance and the limitations for RNA are unclear. In this article, we provide a comprehensive analysis of the performance of AlphaFold3 in the prediction of 3D structures of RNA. Through an extensive benchmark over five different test sets, we discuss the performance and limitations of AlphaFold3. We also compare its performance with ten existing state-of-the-art ab initio, template-based and deep-learning approaches. Our results are freely available on the EvryRNA platform at https://evryrna.ibisc.univ-evry.fr/evryrna/alphafold3/.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"49-62"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11804252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045244","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

Stephen Harrop (1966-2024).

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-02-01 Epub Date: 2025-02-03 DOI: 10.1107/S2059798325000890

Charles S Bond, Paul M G Curmi, John R Helliwell, Alan Riboldi-Tunnicliffe, Rachel M Williamson

引用次数: 0

Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation. 用键价法重新考虑VFe蛋白中的p簇：它们的电子转移和质子化。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-02-01 Epub Date: 2025-01-22 DOI: 10.1107/S2059798325000415

Zhen Lang Xie, Wan Ting Jin, Zhao Hui Zhou

{"title":"Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation.","authors":"Zhen Lang Xie, Wan Ting Jin, Zhao Hui Zhou","doi":"10.1107/S2059798325000415","DOIUrl":"10.1107/S2059798325000415","url":null,"abstract":"P-clusters have been statistically analysed using the bond-valence sum (BVS) method together with weighting schemes. The crystallographic data come from the VFe proteins deposited in the Protein Data Bank (PDB) with high resolutions of better than 1.35 Å. Calculations show that the formal oxidation state of a P1+ cluster can be assigned as 2Fe3+6Fe2+ with high electron delocalization, giving the same oxidation state as that of PN clusters in VFe proteins. Further comprehensive comparisons of the bond distances suggest that the hydroxyl groups of the β-153 serine residues in P1+ and PN clusters are in the protonated state, where the Fe6 atoms have the same oxidation state as Fe2+. During the transition from PN to P1+, cleavage of the Fe6-S1 bond is accompanied by the formation of a weak coordination between the Fe6 atom and the hydroxyl group of the β-153 serine residue in the P1+ cluster of the VFe protein. Similarly, oxidation of PN to P1+/P2+ clusters corresponds to the coordination of Fe6(II) by the hydroxyl group of the β-188 serine residue and of Fe5(II) by the peptide amine group of the α-88 cysteine residue in the MoFe protein of Azotobacter vinelandiis without electron and proton transfers.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"77-84"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998340","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

TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-02-01 DOI: 10.1107/S2059798325000865

Pranav N M Shah, Ruben Sanchez-Garcia, David I Stuart

{"title":"TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms.","authors":"Pranav N M Shah, Ruben Sanchez-Garcia, David I Stuart","doi":"10.1107/S2059798325000865","DOIUrl":"10.1107/S2059798325000865","url":null,"abstract":"Cryo-electron tomography is a rapidly developing field for studying macromolecular complexes in their native environments and has the potential to revolutionize our understanding of protein function. However, fast and accurate identification of particles in cryo-tomograms is challenging and represents a significant bottleneck in downstream processes such as subtomogram averaging. Here, we present tomoCPT (Tomogram Centroid Prediction Tool), a transformer-based solution that reformulates particle detection as a centroid-prediction task using Gaussian labels. Our approach, which is built upon the SwinUNETR architecture, demonstrates superior performance compared with both conventional binary labelling strategies and template matching. We show that tomoCPT effectively generalizes to novel particle types through zero-shot inference and can be significantly enhanced through fine-tuning with limited data. The efficacy of tomoCPT is validated using three case studies: apoferritin, achieving a resolution of 3.0 Å compared with 3.3 Å using template matching, SARS-CoV-2 spike proteins on cell surfaces, yielding an 18.3 Å resolution map where template matching proved unsuccessful, and rubisco molecules within carboxysomes, reaching 8.0 Å resolution. These results demonstrate the ability of tomoCPT to handle varied scenarios, including densely packed environments and membrane-bound proteins. The implementation of the tool as a command-line program, coupled with its minimal data requirements for fine-tuning, makes it a practical solution for high-throughput cryo-ET data-processing workflows.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"63-76"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11804251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187910","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

AlphaFold-guided molecular replacement for solving challenging crystal structures. alphafold引导分子替代解决具有挑战性的晶体结构。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-01-01 DOI: 10.1107/S2059798324011999

Wei Wang, Zhen Gong, Wayne A Hendrickson

{"title":"AlphaFold-guided molecular replacement for solving challenging crystal structures.","authors":"Wei Wang, Zhen Gong, Wayne A Hendrickson","doi":"10.1107/S2059798324011999","DOIUrl":"10.1107/S2059798324011999","url":null,"abstract":"Molecular replacement (MR) is highly effective for biomolecular crystal structure determination, increasingly so as the database of known structures has increased. For candidates without recognizable similarity to known structures, however, crystal structure analyses have nearly always required experiments for de novo phase evaluation. Now, with the unprecedented accuracy of AlphaFold predictions of protein structures from amino-acid sequences, an appreciable expansion of the reach of MR for proteins is realized. Here, we sought to automate an AlphaFold-guided MR procedure that tailors predictions to the MR problem at hand. We first optimized the reliability cutoff parameters for residue inclusion as tested in application to a previously MR-intractable problem. We then examined cases where AlphaFold by default predicts a conformation alternative to that of the candidate structure, devising tests for MR solution either from domain-specific predictions or from predictions based on diverse sequence subclusters. We tested subclustering procedures on an enzyme system that entails multiple MR-challenging conformations. The overall process as implemented in Phenix automatically surveys a succession of trials of increasing computational complexity until an MR solution is found or the options are exhausted. Validated MR solutions were found for 92% of one set of 158 challenging problems from the PDB and 93% of those from a second set of 215 challenges. Thus, many crystal structure analyses that previously required experimental phase evaluation can now be solved by AlphaFold-guided MR. In effect, this and related MR approaches are de novo phasing methods.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"4-21"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875864","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

Making the most of an abundance of data. 充分利用丰富的数据。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-01-01 DOI: 10.1107/S205979832401204X

Christoph Mueller-Dieckmann, Anna J Warren, David G Waterman

引用次数: 0