[English] 日本語
Yorodumi- PDB-2seb: X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2seb | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II | ||||||
Components |
| ||||||
Keywords | COMPLEX (MHC CLASS II/SUPERANTIGEN) / COMPLEX (MHC CLASS II-SUPERANTIGEN) / COMPLEX (MHC CLASS II-SUPERANTIGEN) complex | ||||||
Function / homology | Function and homology information collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / cartilage development involved in endochondral bone morphogenesis ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / cartilage development involved in endochondral bone morphogenesis / regulation of interleukin-4 production / Extracellular matrix organization / notochord development / regulation of interleukin-10 production / limb bud formation / Collagen biosynthesis and modifying enzymes / positive regulation of T cell mediated immune response to tumor cell / 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 / tissue homeostasis / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / endochondral ossification / cellular response to BMP stimulus / Signaling by PDGF / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / NCAM1 interactions / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / collagen fibril organization / cartilage development / intermediate filament / proteoglycan binding / transport vesicle membrane / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / inner ear morphogenesis / T-helper 1 type immune response / polysaccharide binding / cartilage condensation / roof of mouth development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Collagen degradation / Non-integrin membrane-ECM interactions / Generation of second messenger molecules / immunological synapse / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / PD-1 signaling / negative regulation of T cell proliferation / epidermis development / Integrin cell surface interactions / chondrocyte differentiation / detection of bacterium / heart morphogenesis / negative regulation of inflammatory response to antigenic stimulus / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / MHC class II antigen presentation / T cell receptor binding / trans-Golgi network membrane / central nervous system development / skeletal system development / lumenal side of endoplasmic reticulum membrane / sensory perception of sound / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / regulation of gene expression Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dessen, A. / Lawrence, C.M. / Cupo, S. / Zaller, D.M. / Wiley, D.C. | ||||||
Citation | Journal: Immunity / Year: 1997 Title: X-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II. Authors: Dessen, A. / Lawrence, C.M. / Cupo, S. / Zaller, D.M. / Wiley, D.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2seb.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2seb.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 2seb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/2seb ftp://data.pdbj.org/pub/pdb/validation_reports/se/2seb | HTTPS FTP |
---|
-Related structure data
Related structure data | 1sebS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-HLA CLASS II HISTOCOMPATIBILITY ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Drosophila / Cellular location (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: P01903 |
---|---|
#2: Protein | Mass: 22520.021 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Drosophila / Cellular location (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: P13760, UniProt: P01911*PLUS |
-Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 65 molecules DE
#3: Protein | Mass: 28411.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P01552 |
---|---|
#4: Protein/peptide | Mass: 1125.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02458 |
#5: Sugar | ChemComp-NAG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 63 % Description: FURTHER REFINEMENT PERFORMED USING PDB ENTRY 1SE2 | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 Details: 0.1 M NA ACETATE PH 4.6 9 - 14% PEG 4000 0.2 M AMMONIUM ACETATE | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Detector: CCD / Date: Oct 1, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 27635 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.218 / % possible all: 83.7 |
Reflection | *PLUS Num. measured all: 178959 |
Reflection shell | *PLUS % possible obs: 83.7 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SEB Resolution: 2.5→12 Å / Rfactor Rfree error: 0.015 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |