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- PDB-1aqd: HLA-DR1 (DRA, DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITY PROTEI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aqd | ||||||
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Title | HLA-DR1 (DRA, DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITY PROTEIN (EXTRACELLULAR DOMAIN) COMPLEXED WITH ENDOGENOUS PEPTIDE | ||||||
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![]() | COMPLEX (MHC PROTEIN/ANTIGEN) / COMPLEX (MHC PROTEIN-ANTIGEN) / HISTOCOMPATIBILITY ANTIGEN / COMPLEX (MHC PROTEIN-ANTIGEN) complex | ||||||
Function / homology | ![]() regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / polysaccharide binding / CD8-positive, alpha-beta T cell activation / T-helper 1 type immune response / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of insulin secretion involved in cellular response to glucose stimulus / endoplasmic reticulum exit site / humoral immune response / macrophage differentiation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of type II interferon production / TAP binding / Generation of second messenger molecules / immunological synapse / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / epidermis development / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / protein tetramerization / clathrin-coated endocytic vesicle membrane / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / structural constituent of cytoskeleton / positive regulation of T cell cytokine production / cognition / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Interferon alpha/beta signaling / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / defense response to Gram-positive bacterium / immune response / positive regulation of protein phosphorylation / external side of plasma membrane / Golgi membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murthy, V.L. / Stern, L.J. | ||||||
![]() | ![]() Title: The class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding. Authors: Murthy, V.L. / Stern, L.J. #1: ![]() Title: Three Dimensional Structure of a Human Class II Mhc Protein Hla-Dr1 Bound to an Endogenous Peptide Authors: Murthy, V.L. #2: ![]() Title: Crystal Structure of the Human Class II Mhc Protein Hla-Dr1 Complexed with an Influenza Virus Peptide Authors: Stern, L.J. / Brown, J.H. / Jardetzky, T.S. / Gorga, J.C. / Urban, R.G. / Strominger, J.L. / Wiley, D.C. #3: ![]() Title: Three-Dimensional Structure of the Human Class II Histocompatibility Antigen Hla-Dr1 Authors: Brown, J.H. / Jardetzky, T.S. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Strominger, J.L. / Wiley, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315.2 KB | Display | ![]() |
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PDB format | ![]() | 258.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1dlhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Details | THERE ARE FOUR MOLECULES IN THIS COORDINATE SET EACH MOLECULE HAS ONE ALPHA CHAIN : RESIDUES 3-182 EACH MOLECULE HAS ONE BETA CHAIN : RESIDUES 4-190 EACH MOLECULE HAS ONE PEPTIDE CHAIN: RESIDUES 3-14 MOLECULE THREE IS THE MOST WELL DEFINED. MOLECULES 1 - 2 AND 3 - 4 EACH FORM THE SO-CALLED "DIMER OF DIMERS". |
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Components
#1: Protein | Mass: 22222.027 Da / Num. of mol.: 4 / Fragment: SECRETED EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22956.596 Da / Num. of mol.: 4 / Fragment: SECRETED EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1858.045 Da / Num. of mol.: 4 / Fragment: ANTIGENIC PEPTIDE Source method: isolated from a genetically manipulated source Details: HLA-DR1 IS A CLASS II MHC PROTEIN, HLA-A2 IS A CLASS I HISTOCOMPATIBILITY ANTIGEN Source: (gene. exp.) ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 56.2 % | ||||||||||||||||||||
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Crystal grow | pH: 3.5 Details: CRYSTALS GREW AS NEEDLES FROM 10MG/ML HLA-DR1 / PEPTIDE COMPLEX, 15% PEG 4000, 100MM GLYCINE, PH 3.5, AT ROOM TEMPERATURE, OVER ONE WEEK. Temp details: room temp | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 73538 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 37.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.45→2.57 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.331 / % possible all: 70 |
Reflection | *PLUS Num. measured all: 157895 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 70 % / Num. unique obs: 7700 / Num. measured obs: 13661 / Rmerge(I) obs: 0.331 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DLH Resolution: 2.45→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: REFMAC USED IN LATER STAGES OF REFINEMENT.
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Displacement parameters | Biso mean: 40.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→6 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.45→2.57 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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