Acta Crystallographica. Section D, Structural Biology最新文献

InstaMap: instant-NGP for cryo-EM density maps.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-04-01 Epub Date: 2025-03-26 DOI: 10.1107/S2059798325002025

Geoffrey Woollard, Wenda Zhou, Erik H Thiede, Chen Lin, Nikolaus Grigorieff, Pilar Cossio, Khanh Dao Duc, Sonya M Hanson

{"title":"InstaMap: instant-NGP for cryo-EM density maps.","authors":"Geoffrey Woollard, Wenda Zhou, Erik H Thiede, Chen Lin, Nikolaus Grigorieff, Pilar Cossio, Khanh Dao Duc, Sonya M Hanson","doi":"10.1107/S2059798325002025","DOIUrl":"10.1107/S2059798325002025","url":null,"abstract":"Despite the parallels between problems in computer vision and cryo-electron microscopy (cryo-EM), many state-of-the-art approaches from computer vision have yet to be adapted for cryo-EM. Within the computer-vision research community, implicits such as neural radiance fields (NeRFs) have enabled the detailed reconstruction of 3D objects from few images at different camera-viewing angles. While other neural implicits, specifically density fields, have been used to map conformational heterogeneity from noisy cryo-EM projection images, most approaches represent volume with an implicit function in Fourier space, which has disadvantages compared with solving the problem in real space, complicating, for instance, masking, constraining physics or geometry, and assessing local resolution. In this work, we build on a recent development in neural implicits, a multi-resolution hash-encoding framework called instant-NGP, that we use to represent the scalar volume directly in real space and apply it to the cryo-EM density-map reconstruction problem (InstaMap). We demonstrate that for both synthetic and real data, InstaMap for homogeneous reconstruction achieves higher resolution at shorter training stages than five other real-spaced representations. We propose a solution to noise overfitting, demonstrate that InstaMap is both lightweight and fast to train, implement masking from a user-provided input mask and extend it to molecular-shape heterogeneity via bending space using a per-image vector field.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"147-169"},"PeriodicalIF":2.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707902","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

Duplicate entries in the Protein Data Bank: how to detect and handle them.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-04-01 Epub Date: 2025-03-08 DOI: 10.1107/S2059798325001883

Alexander Wlodawer, Zbigniew Dauter, Pawel Rubach, Wladek Minor, Mariusz Jaskolski, Ziqiu Jiang, William Jeffcott, Olga Anosova, Vitaliy Kurlin

引用次数: 0

Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-04-01 Epub Date: 2025-03-17 DOI: 10.1107/S2059798325002141

Shuping Zheng, Xiangrui Shi, Junjin Lin, Yiwei Yang, Yiting Xin, Xinru Bai, Huachen Zhu, Hui Chen, Jiasen Wu, Xiaowei Zheng, Ling Lin, Zhihong Huang, Sheng Yang, Fen Hu, Wei Liu

{"title":"Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein.","authors":"Shuping Zheng, Xiangrui Shi, Junjin Lin, Yiwei Yang, Yiting Xin, Xinru Bai, Huachen Zhu, Hui Chen, Jiasen Wu, Xiaowei Zheng, Ling Lin, Zhihong Huang, Sheng Yang, Fen Hu, Wei Liu","doi":"10.1107/S2059798325002141","DOIUrl":"10.1107/S2059798325002141","url":null,"abstract":"Green-to-red photoconvertible fluorescent proteins (PCFPs) serve as key players in single-molecule localization super-resolution imaging. As an early engineered variant, mEos3.2 has limited applications, mostly due to its slow maturation rate. The recent advent of a novel variant, pcStar, obtained by the simple mutation of only three amino acids (D28E/L93M/N166G) in mEos3.2, exhibits significantly accelerated maturation and enhanced fluorescent brightness. This improvement represents an important advance in the field of biofluorescence by enabling early detection with reliable signals, essential for labelling dynamic biological processes. However, the mechanism underlying the significant improvement in fluorescent performance from mEos3.2 to pcStar remains elusive, preventing the rational design of more robust variants through mutagenesis. In this study, we determined the crystal structures of mEos3.2 and pcStar in their green states at atomic resolution and performed molecular-dynamics simulations to reveal significant divergences between the two proteins. Our structural and computational analyses revealed crucial features that are distinctively present in pcStar, including the presence of an extra solvent molecule, high conformational stability and enhanced interactions of the chromophore with its surroundings, tighter tertiary-structure packing and dynamic central-helical deformation. Resulting from the triple mutations, all of these structural features are likely to establish a mechanistic link to the greatly improved fluorescent performance of pcStar. The data described here not only provide a good example illustrating how distant amino-acid substitutions can affect the structure and bioactivity of a protein, but also give rise to strategic considerations for the future engineering of more widely applicable PCFPs.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"181-195"},"PeriodicalIF":2.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646712","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

Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern.

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2025-04-01 Epub Date: 2025-03-24 DOI: 10.1107/S2059798325002190

Hiroyuki Iwamoto

{"title":"Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern.","authors":"Hiroyuki Iwamoto","doi":"10.1107/S2059798325002190","DOIUrl":"10.1107/S2059798325002190","url":null,"abstract":"The contractile machinery of muscle, especially that of skeletal muscle, has a very regular array of contractile protein filaments, and gives rise to a complex and informative diffraction pattern when irradiated with X-rays. However, analyzing these diffraction patterns is often challenging because (i) only rotationally averaged diffraction patterns can be obtained, resulting in a substantial loss of information, and (ii) the contractile machinery contains two different sets of protein filaments (actin and myosin) with different helical symmetries. The reflections originating from them often overlap. These problems may be solved if the real-space 3D structure of the contractile machinery is directly calculated from the diffraction pattern. Here, we demonstrate that by using the conventional phase-retrieval algorithm (hybrid input-output), the real-space 3D structure of the contractile machinery can be effectively restored from a single rotationally averaged 2D diffraction pattern. In this calculation, we used an in silico model of insect flight muscle, which is known for its highly regular structure. We also extended this technique to an experimentally recorded muscle diffraction pattern.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"196-206"},"PeriodicalIF":2.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690823","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

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