+Open data
-Basic information
Entry | Database: PDB / ID: 7o00 | ||||||||||||
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Title | Crystal structure of HLA-DR4 in complex with a HSP70 peptide | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex / MHCII | ||||||||||||
Function / homology | Function and homology information bacterial extracellular vesicle / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation ...bacterial extracellular vesicle / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / unfolded protein binding / Downstream TCR signaling / positive regulation of T cell activation / protein folding / MHC class II protein complex binding / late endosome membrane / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / lysosomal membrane / Golgi membrane / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||||||||
Authors | Ge, C. / Holmdahl, R. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: Ann Rheum Dis / Year: 2022 Title: Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor. Authors: Ge, C. / Weisse, S. / Xu, B. / Dobritzsch, D. / Viljanen, J. / Kihlberg, J. / Do, N.N. / Schneider, N. / Lanig, H. / Holmdahl, R. / Burkhardt, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o00.cif.gz | 291.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o00.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7o00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o00_validation.pdf.gz | 761 KB | Display | wwPDB validaton report |
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Full document | 7o00_full_validation.pdf.gz | 765.9 KB | Display | |
Data in XML | 7o00_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 7o00_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/7o00 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/7o00 | HTTPS FTP |
-Related structure data
Related structure data | 7nzeC 7nzfC 7nzhC 1j8hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-HLA class II histocompatibility ... , 2 types, 2 molecules AAABBB
#1: Protein | Mass: 20598.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903 |
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#2: Protein | Mass: 22218.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: A0A1V1IGJ9 |
-Protein/peptide / Non-polymers , 2 types, 81 molecules CCC
#3: Protein/peptide | Mass: 1520.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: A1KFH2 |
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#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 290 K / Method: evaporation Details: 0.03 M of each divalent cation (12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD), 0.1 M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.24→56.89 Å / Num. obs: 25047 / % possible obs: 99.8 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.066 / Rrim(I) all: 0.246 / Net I/σ(I): 12 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J8H Resolution: 2.24→51.453 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.175 / SU B: 16.37 / SU ML: 0.179 / Average fsc free: 0.88 / Average fsc work: 0.8927 / Cross valid method: FREE R-VALUE / ESU R: 0.284 / ESU R Free: 0.221 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.581 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→51.453 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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