Acta Crystallographica. Section D, Structural Biology最新文献

Separating the effects of temperature and absorbed X-ray dose on unit-cell volume. 分离温度和x射线吸收剂量对单位细胞体积的影响。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-10-01 Epub Date: 2026-09-15 DOI: 10.1107/S2059798326008612

Robert J Southworth-Davies, James W Murray, Ian Carmichael, Enrique Rudiño-Piñera, Martin Weik, Elspeth F Garman

引用次数: 0

A short history of Auto-Rickshaw. 三轮车的历史简史。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-10-01 Epub Date: 2026-09-22 DOI: 10.1107/S2059798326008831

Santosh Panjikar, Victor Lamzin, Paul A Tucker, Manfred S Weiss

{"title":"A short history of Auto-Rickshaw.","authors":"Santosh Panjikar, Victor Lamzin, Paul A Tucker, Manfred S Weiss","doi":"10.1107/S2059798326008831","DOIUrl":"10.1107/S2059798326008831","url":null,"abstract":"Auto-Rickshaw was developed in the early 2000s at EMBL Hamburg as an automated macromolecular structure-determination platform for crystallography and structural biology. Its initial motivation was to provide beamline users with rapid feedback on whether diffraction data were sufficient for structure solution. The platform was not merely a wrapper around existing crystallographic programs; it encoded the expert decisions needed to select phasing, density-modification, model-building and refinement protocols according to the information available from the experiment. Since its first publication in 2005, Auto-Rickshaw has supported a broad range of experimental and model-based strategies, including SAD, MAD, SIR, SIRAS, RIP, molecular replacement and hybrid approaches such as MRSAD. A central feature was the integration of the SHELX programs, particularly SHELXC, SHELXD and SHELXE, whose speed, robustness and command-line design made them especially suitable for automated pipelines. This review gives a brief historical account of Auto-Rickshaw, the beamline context in which it emerged, the design principles that shaped it and the role of SHELX programs in its phasing architecture. It also considers the broader legacy of Auto-Rickshaw as a bridge between crystallographic expertise and automated, reproducible structure solution. Finally, the review places Auto-Rickshaw in the current landscape of synchrotron technologies, high-throughput structural biology, containerized deployment, predicted structural models and AI-assisted decision making, where reliable automation remains essential.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1139-1151"},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13632750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015129","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

Radiation damage in serial femtosecond crystallography studied in hemoglobin. 连续飞秒晶体学研究血红蛋白的辐射损伤。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-10-01 Epub Date: 2026-09-30 DOI: 10.1107/S2059798326008569

Marina Galchenkova, Ibrahim Dawod, Sebastian Cardoch, Janina Sprenger, Dominik Oberthür, Salah Awel, Emiliano De Santis, Oscar Grånäs, Juraj Knoska, Markus Metz, Spencer Passmore, Gisel Pena, Iosifina Sarrou, Max Wiedorn, Nicusor Timneanu, Henry Chapman, Oleksandr Yefanov, Carl Caleman

{"title":"Radiation damage in serial femtosecond crystallography studied in hemoglobin.","authors":"Marina Galchenkova, Ibrahim Dawod, Sebastian Cardoch, Janina Sprenger, Dominik Oberthür, Salah Awel, Emiliano De Santis, Oscar Grånäs, Juraj Knoska, Markus Metz, Spencer Passmore, Gisel Pena, Iosifina Sarrou, Max Wiedorn, Nicusor Timneanu, Henry Chapman, Oleksandr Yefanov, Carl Caleman","doi":"10.1107/S2059798326008569","DOIUrl":"10.1107/S2059798326008569","url":null,"abstract":"A central question in macromolecular crystallography is what X-ray free-electron laser pulse duration is required to obtain damage-free structural information. We compare serial femtosecond crystallography data from hemoglobin crystals using 3 and 10 fs pulses at comparable peak intensities (∼3 × 1017 W cm-2) and fixed photon energy (7.15 keV). Structural refinement produced very similar models and resolution-dependent data-quality indicators remained comparable. Both datasets also retained sufficient anomalous signal for phasing. These observations support the conclusion that high-resolution scattering was preserved under both pulse durations. Hybrid collisional-radiative and molecular-dynamics simulations show that under typical experimental conditions, atomic form-factor changes are negligible (<1%) and atomic displacements fall below the resolution limit imposed by the X-ray photon energy and the geometry of the detector. The combined experimental and theoretical results indicate that 10 fs pulses are adequate to obtain damage-free protein structures using femtosecond crystallography under the intensity conditions explored.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1169-1180"},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13632746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079159","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

On-grid enrichment strategies in cryo-EM: affinity-functionalized supports for low-abundance and challenging targets. 低温电镜中的网格富集策略：低丰度和挑战性目标的亲和功能化支持。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-10-01 Epub Date: 2026-09-24 DOI: 10.1107/S2059798326009605

Pankhi Mili, Oikyam Jyotish Chetia, Uddipan Das

{"title":"On-grid enrichment strategies in cryo-EM: affinity-functionalized supports for low-abundance and challenging targets.","authors":"Pankhi Mili, Oikyam Jyotish Chetia, Uddipan Das","doi":"10.1107/S2059798326009605","DOIUrl":"10.1107/S2059798326009605","url":null,"abstract":"Cryo-electron microscopy (cryo-EM) has become a leading method for high-resolution structural analysis of biological macromolecules. Despite major advances in instrumentation and image processing, specimen preparation remains a critical bottleneck, particularly for membrane proteins, endogenous assemblies, chromatin-associated complexes and transient signaling intermediates. These targets are often available only in limited quantities and are susceptible to denaturation, dissociation and preferred orientation during conventional grid preparation. Affinity-functionalized grids have emerged as a powerful specimen-preparation strategy that enables selective on-grid capture, enrichment and purification prior to vitrification, thereby increasing the local particle concentration, improving particle recovery and, in some implementations, reducing exposure to the air-water interface. Here, we review affinity-functionalized and engineered cryo-EM supports as a unified class of specimen-preparation technologies and compare the major validated platforms, including nickel-nitrilotriacetic acid (Ni-NTA) lipid monolayers, streptavidin affinity grids, antibody-based supports, graphene-derived substrates and magnetic nanoparticle-based enrichment systems. We discuss their strengths, limitations and applications, as well as emerging developments in programmable capture chemistries, automated vitrification workflows and in situ structural biology. Collectively, these technologies are transforming the cryo-EM support from a passive substrate into an active biochemical interface, expanding the range of biological systems accessible to structural investigation.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1125-1138"},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035976","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

Single-crystal X-ray and in crystallo XANES studies resolve cobalt coordination in cobalamin and rule out radiation-induced ligand loss in human intrinsic factor. 单晶x射线和晶体XANES研究解决了钴胺素中的钴配位，并排除了辐射引起的人体内在因素中的配体损失。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-10-01 Epub Date: 2026-09-14 DOI: 10.1107/S2059798326007539

Narayanasami Sukumar, David H Alpers, George E Sterbinsky, Sahana L Sukumar

{"title":"Single-crystal X-ray and in crystallo XANES studies resolve cobalt coordination in cobalamin and rule out radiation-induced ligand loss in human intrinsic factor.","authors":"Narayanasami Sukumar, David H Alpers, George E Sterbinsky, Sahana L Sukumar","doi":"10.1107/S2059798326007539","DOIUrl":"10.1107/S2059798326007539","url":null,"abstract":"Human intrinsic factor (IF) mediates the intestinal uptake of cobalamin (Cbl; vitamin B12). A previous crystal structure of the IF-cobalamin complex revealed the apparent absence of an upper axial ligand at the cobalt center, raising questions regarding radiation-induced cleavage or chemical modification during crystallization. Here, high-resolution single-crystal X-ray crystallography of cobalamin in three states, oxidized and two independently prepared chemically reduced crystals, resolves clear electron density for an intact axial cyanide ligand at the cobalt center in all cases, including a crystal previously subjected to X-ray exposure during spectroscopic measurement. In crystallo Co K-edge X-ray absorption near-edge structure (XANES) spectroscopy performed on the same crystals shows a shift in absorption-edge energy compatible with, but not independently diagnostic of, partial chemical reduction, while indicating the retention of six-coordinate cobalt geometry in both states. Correlation of the spectroscopic and crystallographic data shows that radiation-induced photolysis of the Co-CN bond is unlikely to explain the apparent absence of axial electron density previously reported for IF-bound cobalamin. These results establish in crystallo XANES as a useful complement to macromolecular crystallography for resolving ambiguities in metalloprotein active-site chemistry, while demonstrating that the crystallographic data alone provide the most direct evidence for ligand retention.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1195-1202"},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13632749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148962783","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 protein epiphany. 蛋白质的顿悟。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-10-01 Epub Date: 2026-09-22 DOI: 10.1107/S2059798326008739

Eleanor Dodson

引用次数: 0

Towards routine accurate electron-density studies of biological macromolecules. 迈向常规精确的生物大分子电子密度研究。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-09-01 Epub Date: 2026-08-12 DOI: 10.1107/S2059798326007448

Elham Paknia, Claus Flensburg, Michal Leszek Chodkiewicz, Rasmus H Fogh, Peter Keller, Clemens Vonrhein, Clemens Schulze-Briese, Paulina Maria Dominiak, Gleb Bourenkov, Gérard Bricogne, Ashwin Chari

{"title":"Towards routine accurate electron-density studies of biological macromolecules.","authors":"Elham Paknia, Claus Flensburg, Michal Leszek Chodkiewicz, Rasmus H Fogh, Peter Keller, Clemens Vonrhein, Clemens Schulze-Briese, Paulina Maria Dominiak, Gleb Bourenkov, Gérard Bricogne, Ashwin Chari","doi":"10.1107/S2059798326007448","DOIUrl":"10.1107/S2059798326007448","url":null,"abstract":"We report here the structure of Pyrococcus abyssi rubredoxin determined at a resolution of 0.43 Å. This, to the best of our knowledge, represents the highest resolution protein structure yet determined. Experimentally, the determination of this structure has been made possible by a series of technical innovations and streamlined procedures that are described herein. The structure model refined with spherical scattering factors, the so-called independent atom model (IAM), reveals many positive difference densities that can be attributed to electrons at the midpoint of chemical bonds. To validate the interpretation that these do indeed represent bonding electrons, we have connected the DiSCaMB transferable aspherical atom model (TAAM) library to BUSTER. TAAM refinements resolve all positive density features in midpoints of chemical bonds. Extrapolating the findings and methodology reported here, we anticipate that it should now be possible to routinely acquire accurate X-ray diffraction data for quantum crystallography of biological macromolecules. This is particularly relevant to the study of enzyme mechanisms, which are well documented to entail quantum-mechanical phenomena.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1044-1055"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148711018","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 basis for T-cell receptor recognition of p53^Y220D, a human cancer neoantigen. 人肿瘤新抗原p53Y220D的t细胞受体识别的结构基础

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-09-01 Epub Date: 2026-08-14 DOI: 10.1107/S2059798326007564

Zhihui Duan, Jianfeng Zhao, Junping Wu, Yue Zhang, Ping Yuan, Yayun Zeng, Huimin Jin, Roy A Mariuzza, Daichao Wu

{"title":"Structural basis for T-cell receptor recognition of p53Y220D, a human cancer neoantigen.","authors":"Zhihui Duan, Jianfeng Zhao, Junping Wu, Yue Zhang, Ping Yuan, Yayun Zeng, Huimin Jin, Roy A Mariuzza, Daichao Wu","doi":"10.1107/S2059798326007564","DOIUrl":"10.1107/S2059798326007564","url":null,"abstract":"Adoptive cell therapy (ACT) with tumor-specific T cells can mediate durable cancer regression. The main target of tumor-specific T cells are neoantigens resulting from mutations in self-antigens over the course of malignant transformation. To understand T-cell recognition of cancer neoantigens at the atomic level, we studied a T-cell receptor (TCR 4414A) that recognizes a neoepitope arising from a driver mutation in the p53 oncogene (p53Y220D) presented by HLA-A2. Here, we report the structure of TCR 4414A bound to HLA-A2 and p53Y220D, as well as structures of unbound wild-type and mutant p53-HLA-A2 ligands. The structures reveal that the Y220D mutation induces a conformational change in the p53Y220D neoepitope that is detected by TCR 4414A, thereby rendering a normally cryptic self-peptide visible to T cells. The TCR minimizes interactions with the N- and C-terminal portions of p53Y220D, which are identical in mutant and wild-type peptides, and instead focuses on the Y220D driver mutation at the peptide center. In this way, TCR 4414A achieves highly specific recognition of mutant over wild-type p53, a critical parameter for avoiding off-target toxicities in ACT.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1082-1092"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148757327","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

Avoiding pitfalls when modelling ligands in macromolecular crystallography. 避免陷阱时建模配体在大分子晶体学。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-09-01 Epub Date: 2026-08-12 DOI: 10.1107/S2059798326007047

Oliver S Smart, Andrew Sharff, Claus Flensburg, Clemens Vonrhein, Gérard Bricogne

{"title":"Avoiding pitfalls when modelling ligands in macromolecular crystallography.","authors":"Oliver S Smart, Andrew Sharff, Claus Flensburg, Clemens Vonrhein, Gérard Bricogne","doi":"10.1107/S2059798326007047","DOIUrl":"10.1107/S2059798326007047","url":null,"abstract":"The determination of protein-ligand complex structures by X-ray crystallography is a cornerstone of modern structure-guided drug discovery. However, the process is complex and fraught with potential pitfalls at every stage, from data collection to final model deposition. The presence of flawed or misinterpreted ligand models in the Protein Data Bank (PDB) can misdirect scientific efforts that rely on them as the basis for new hypotheses and experiments. This article outlines a practical approach for ligand validation during structure determination. We discuss the application of validation tools, such as those in Coot, MolProbity, Mogul and Buster-report, to avoid errors. By re-examining several deposited PDB entries, we illustrate key pitfalls, including (i) modelling a ligand into absent or ambiguous electron density, (ii) incorrect chemical definitions (e.g. chirality, tautomers), (iii) poor fit of parts of a ligand to the electron density and (iv) data/model mismatches during deposition. We emphasize the importance of a `null-hypothesis' approach and continuous critical assessment throughout the modelling process to improve the reliability of deposited structures.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1016-1029"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148710983","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

Structure and allostery in major facilitator superfamily symport mechanisms. 主要促进剂超族同调机制的结构与变构。

IF 4.3 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-09-01 Epub Date: 2026-08-21 DOI: 10.1107/S2059798326007485

Lan Guan

{"title":"Structure and allostery in major facilitator superfamily symport mechanisms.","authors":"Lan Guan","doi":"10.1107/S2059798326007485","DOIUrl":"10.1107/S2059798326007485","url":null,"abstract":"The solute carriers of the major facilitator superfamily (MFS) play significant roles in human health and disease. The melibiose transporter of Salmonella enterica serovar Typhimurium (MelBSt) catalyzes the stoichiometric symport of galactosides with Na+, H+ or Li+ and is a well studied prototype of MFS transporters. With a large body of data from extensive functional analyses using multiple transport and binding assays, structural characterizations of multiple states by X-ray crystallography and cryoEM single-particle analysis, and dynamic elucidations using hydrogen-deuterium exchange mass spectrometry (HDX-MS), the molecular recognition of the primary substrate galactoside and its coupling cation Na+, H+ or Li+ has been elucidated at the molecular level. Cooperative binding of both solutes is recognized as the core symport mechanism that supports the transporter's functions more effectively in a sugar-scarce environment. Structural and dynamic studies show that conformational dynamics significantly influence sugar binding but have minimal effect on Na+. Na+ acts as an allosteric activator, increasing sugar affinity by stabilizing the inner barrier and constraining conformational flexibility. All data are consistent with the previously constructed stepped-binding kinetic model for melibiose symport with Na+; in addition, MFS uniport and antiport mechanisms are discussed.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1030-1043"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786876","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