Acta Crystallographica Section D最新文献

{"title":"Crystal structure of the β2-microglobulin-BBM.1 antibody complex reveals the molecular basis of antigen recognition.","authors":"Jiajia Wu,Fuming Zeng,Xiaorong Wang,Pengcheng Wei","doi":"10.1107/s2059798325006370","DOIUrl":"https://doi.org/10.1107/s2059798325006370","url":null,"abstract":"β2-Microglobulin (β2M) is an essential component of major histocompatibility complex class I (MHC-I) molecules, with a well established canonical role in immune surveillance. Beyond its classical functions, accumulating evidence has highlighted β2M as a multifaceted biomarker, with elevated serum levels closely associated with disease burden and prognosis in metabolic disorders, malignancies, autoimmune diseases and central nervous system conditions. In this study, we resolved the crystal structure of human β2M in complex with the mouse monoclonal antibody BBM.1 at 2.50 Å resolution using X-ray crystallography. Structural analysis revealed that BBM.1 binds β2M through multiple CDRs, recognizing key surface residues including Glu36, Asp38, Lys41, Asn42, Glu44, Arg45, Glu47 and Arg81. The interaction is anchored by a central hydrophobic core formed by Trp32 (light chain), Trp99 (heavy chain) and Ile92 (β2M), which is deeply buried in the interface. Surrounding this core is a well organized polar interaction network composed of hydrogen bonds and salt bridges, primarily involving β2M residues Lys41, Glu44, Arg45 and Glu47. Notably, the Arg45 residue deeply embeds into the antibody-binding pocket, forming several crucial interactions. These findings not only validate previous biochemical and mutational data but also identify new epitope residues, providing a structural foundation for the development and optimization of precision therapeutic strategies targeting β2M.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756183","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}

{"title":"Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.","authors":"Cong T S Van,Cyril F Reboul,Joseph J E Caesar,Rubén Meana-Pañeda,George T Lountos,Justin C Deme,Owain J Bryant,Steven Johnson,Claire T Piczak,Eugene Valkov,Susan M Lea,Hans Elmlund","doi":"10.1107/s2059798325005686","DOIUrl":"https://doi.org/10.1107/s2059798325005686","url":null,"abstract":"Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires ab initio 3D reconstruction of density volume(s) from 2D images (particles). This large-scale inverse problem requires the determination of many million degrees of freedom from extremely noisy experimental measurements. Here, we introduce a new approach to probabilistic multi-volume ab initio 3D reconstruction for simultaneous estimation of the relative particle 3D orientations and partitioning of the particles into groups with distinct structural states. To account for further structural variability within the discrete state groups, due to for example regional disorder, flexibility or partial occupancy of associating ligands, we introduce a new method for adaptive non-uniform regularization based on iterated conditional modes (ICMs). Our ICM regularization approach can be viewed as a spatially varying real-space prior that optimizes the connectivity of the reconstructed density map(s). Our method is designed to run in real time as the microscope collects the data, which puts significant constraints on algorithm scalability and flexibility with regard to how new particles are incorporated. We describe the probabilistic optimization and non-uniform regularization theory in detail. Finally, we provide numerous benchmarking examples, both on publicly available standard test data sets and on data sets acquired at our cryo-EM facility at the National Cancer Institute, National Institutes of Health. The implementation of our new multi-volume ab initio 3D reconstruction approach is part of the SIMPLE software suite, which is provided open source at https://github.com/hael/SIMPLE.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"694 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568501","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}

{"title":"Perspective on a large-scale ligand structure characterization.","authors":"Elspeth F Garman","doi":"10.1107/s2059798325006631","DOIUrl":"https://doi.org/10.1107/s2059798325006631","url":null,"abstract":"An introduction to a set of three related papers in this issue describing 216 ligand-bound fatty acid-binding protein structure determinations and the pitfalls that can arise in such a study.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"27 1","pages":"394-395"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756280","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}

{"title":"A high-resolution data set of fatty acid-binding protein structures. I. Dynamics of FABP4 and ligand binding.","authors":"Fabio Casagrande,Andreas Ehler,Dominique Burger,Joerg Benz,Alfred Ross,Markus G Rudolph","doi":"10.1107/s2059798325006242","DOIUrl":"https://doi.org/10.1107/s2059798325006242","url":null,"abstract":"Fatty acid-binding proteins (FABPs) are involved in the uptake and intracellular trafficking of fatty acids for metabolic and gene-regulatory purposes. FABPs are known to associate with membranes and also enter the nucleus. Using NMR and a human FABP4 (hFABP4) preparation completely free of endogenous ligands, we studied the influence of fatty acids and inhibitors on the conformational flexibility and bicelle/membrane association of this isoform. Binding of fatty acids and ligands rigidifies hFABP4, particularly at the portal region where ligands enter the binding site. Depending on the nature of the ligand, hFABP4 stays associated with bicelles via the portal region or segregates into solution, a prerequisite for nuclear import using a nonclassical nuclear localization signal. These results indicate that different ligands can lead to different biological outcomes. One of the major determinants for FABP4 segregation is Phe58, which in X-ray crystal structures adopts different conformations as a function of ligand volume. It is possible that other FABP isoforms use a similar mechanism for ligand-dependent membrane detachment and activation of nuclear import.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"14 1","pages":"423-435"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756283","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}

{"title":"A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.","authors":"Andreas Ehler,Christian Bartelmus,Joerg Benz,Inken Plitzko,Markus G Rudolph","doi":"10.1107/s2059798325006096","DOIUrl":"https://doi.org/10.1107/s2059798325006096","url":null,"abstract":"FABP4 has been implicated as a therapeutic target for treating diabetes and atherosclerosis. Structure-based drug design (SBDD) based on initial hits from high-throughput and fragment screens yielded 216 ligand-bound structures of human FABP3, FABP4 and FABP5 isoforms, many of which were at resolutions of better than 1.2 Å. An estimated 15% of the ligands had a different chemical composition to that expected from the starting materials or the final synthesis product, highlighting a potential problem inherent to all SBDD campaigns conducted at lower resolution. Apart from possible human error during compound registration, side reactions such as additions, eliminations, isomerizations, cyclizations and dimerizations were found that led to compounds capable of binding to FABP.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"286 1","pages":"451-464"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756281","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}

{"title":"A high-resolution data set of fatty acid-binding protein structures. II. Crystallographic overview, ligand classes and binding pose.","authors":"Andreas Ehler,Joerg Benz,Markus G Rudolph","doi":"10.1107/s2059798325005728","DOIUrl":"https://doi.org/10.1107/s2059798325005728","url":null,"abstract":"Fatty acid-binding protein isoforms 4 and 5 are potential diabetes and atherosclerosis targets. During a drug-design program aiming at dual isoform-specific FABP4/5 inhibitors with little or no affinity for FABP3, a set of crystal structures with a median resolution of 1.2 Å was generated. The chemical space of the ligands covers various series in which the carboxylate and aliphatic groups of the natural fatty-acid ligands have been replaced by other moieties. A summary of binding modes of the chemical series is also given with respect to how isoform specificity was achieved. Additionally, several bromine-containing ligands were identified that allowed SAD phasing, yielding an independent experimental confirmation of their chemical composition.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"27 1","pages":"436-450"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756306","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}

{"title":"Enhanced capabilities for multi-crystal data collection based on double mesh scans.","authors":"Igor Melnikov,Olof Svensson,Gleb Bourenkov,Alexander Popov","doi":"10.1107/s2059798325005145","DOIUrl":"https://doi.org/10.1107/s2059798325005145","url":null,"abstract":"Two-dimensional X-ray mesh (raster) scans are broadly used in macromolecular crystallography to identify positions on the sample holder at which diffraction images can be collected. Based on a single mesh scan, the commonly known method Mesh&Collect allows the collection of small angular wedges of diffraction data from multiple crystals identified in the mesh-scan area. Recently, the capabilities of the method have been extended by using two mesh scans instead of one. The scans are usually performed at orthogonal orientations of the rotation axis, or any other angular difference less than 90° can be used. This allows the more accurate determination, when compared with a single mesh scan, of the 3D centre positions of each crystal contained in the scanned area and gives better estimates of their dimensions and diffraction qualities. We present the upgraded DoubleMesh&Collect method based on the Dozor, Dozor-m2 and Resheteau software programs which automatically analyse the diffraction images of the two mesh scans. The applicability of the method is demonstrated on several cases, including room-temperature diffraction studies. The problem of cartography of large crystals is discussed.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488178","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}

{"title":"Structural dynamics of IDR interactions in human SFPQ and implications for liquid-liquid phase separation.","authors":"Heidar J Koning,Valerie Lai,Ashish Sethi,Shatabdi Chakraborty,Ching Seng Ang,Archa H Fox,Anthony P Duff,Andrew E Whitten,Andrew C Marshall,Charles S Bond","doi":"10.1107/s2059798325005303","DOIUrl":"https://doi.org/10.1107/s2059798325005303","url":null,"abstract":"The proteins SFPQ (splicing factor proline- and glutamine-rich) and NONO (non-POU domain-containing octamer-binding protein) are members of the Drosophila behaviour/human splicing (DBHS) protein family, sharing 76% sequence identity in their conserved DBHS domain. These proteins are critical for elements of pre- and post-transcriptional regulation in mammals and are primarily located in paraspeckles: ribonucleoprotein bodies templated by NEAT1 long noncoding RNA. Regions that are structured and predicted to be disordered (IDRs) in DBHS proteins facilitate various interactions, including dimerization, polymerization, nucleic acid binding and liquid-liquid phase separation, all of which have consequences for cell health, the pathology of some neurological diseases and cancer. To date, very limited structural work has been carried out on characterizing the IDRs of the DBHS proteins, largely due to their predicted disordered nature and the fact that this is often a bottleneck for conventional structural techniques. This is a problem worth addressing, as the IDRs have been shown to be critical to the material state of the protein as well as its function. In this study, we used small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), together with lysine cross-linking mass spectrometry (XL-MS), to investigate the regions of SFPQ flanking the structured DBHS domain and the possibility of dimer partner exchange of full-length proteins. Our results demonstrate experimentally that the N- and C-terminal regions on either side of the folded DBHS domain are long, disordered and flexible in solution. Realistic modelling of disordered chains to fit the scattering data and the compaction of the different protein variants suggests that it is physically possible for the IDRs to be close enough to interact. The mass-spectrometry data additionally indicate that the C-terminal IDR can potentially interact with the folded DBHS domain and also shares some conformational space with the N-terminal IDR. Our small-angle neutron scattering (SANS) experiments reveal that full-length SFPQ is capable of swapping dimer partners with itself, which has implications for our understanding of the combinatorial dimerization of DBHS proteins within cells. Our study provides insight into possible interactions between different IDRs either in cis or in trans and how these may relate to protein function, and the possible impact of mutations in these regions. The dynamic dimer partner exchange of a full-length protein inferred from this study is a phenomenon that is integral to the function of DBHS proteins, allowing changes in gene-regulatory activity by altering levels of the various heterodimers or homodimers.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504630","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}

{"title":"Crystal structure of coagulation factor XII N-terminal domains 1-5.","authors":"Muhammad Saleem,Chan Li,Bubacarr G Kaira,Alexander K Brown,Monika Pathak,Shabir Najmudin,Nathan Cowieson,Ingrid Dreveny,Clare Wilson,Aleksandr Shamanaev,David Gailani,Stephanie A Smith,James H Morrissey,Helen Philippou,Jonas Emsley","doi":"10.1107/s2059798325005297","DOIUrl":"https://doi.org/10.1107/s2059798325005297","url":null,"abstract":"Factor XIIa (FXIIa) is generated from its zymogen factor XII (FXII) by contact with polyanions such as inorganic polyphosphates. FXIIa cleaves the substrates prekallikrein and factor XI, triggering inflammatory cascades and plasma coagulation. From the N-terminus, FXII has fibronectin type II (FnII), epidermal growth factor-1 (EGF1), fibronectin type I (FnI), EGF2 and kringle domains. The N-terminal domains of FXII mediate polyanion and Zn2+ binding. To understand how ligand binding to polyanions and Zn2+ is coordinated across multiple domains, we determined the crystal structure of recombinant FXII domains 1-5 (FXIIHC5) to 3.4 Å resolution. A separate crystal structure of the isolated FXII FnII domain at 1.2 Å resolution revealed two bound Zn2+ ions. In FXIIHC5 a head-to-tail interaction is formed between the FnII and kringle domains, co-localizing the lysine-binding sites of the kringle domain and the cation-binding site of the FnII domain. Two FXIIHC5 monomers interlock, burying a large surface area of 2067 Å2, such that two kringle domains point outwards separated by a distance of 20 Å. The polyanion-binding site in the EGF1 domain is localized onto a plane together with the FnII and FnI domains. Using native mass spectrometry, we detected a major FXIIHC5 monomer peak and a minor dimer peak. Small-angle X-ray scattering and gel-filtration chromatography revealed the presence of monomers and dimers in solution. These FXII N-terminal domain structures provide a holistic framework to understand how the mosaic domain structure of FXII assembles diverse ligand-binding sites in three dimensions.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504629","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}

{"title":"Image-processing methods for electron microscopy of biological specimens.","authors":"Carlos Oscar S Sorzano,Albert Bartesaghi,Amit Singer","doi":"10.1107/s2059798325004449","DOIUrl":"https://doi.org/10.1107/s2059798325004449","url":null,"abstract":"The focused issue on Image-processing methods for electron microscopy of biological specimens is introduced. The virtual issue is available at https://journals.iucr.org/special_issues/2025/imageprocessing.","PeriodicalId":501686,"journal":{"name":"Acta Crystallographica Section D","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087645","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}