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Open data
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Basic information
| Entry | Database: PDB / ID: 8vcx | |||||||||
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| Title | Human TCR A2.13 in complex with DQ8-InsCpep | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Immune receptor complex | |||||||||
| Function / homology | Function and homology informationantigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion ...antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / MHC class II protein complex / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / lysosomal membrane / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | Tran, T.M. / Lim, J.J. / Loh, T.J. / Mannering, I.S. / Rossjohn, J. / Reid, H.H. | |||||||||
| Funding support | Australia, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2024Title: A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8. Authors: Tran, M.T. / Lim, J.J. / Loh, T.J. / Mannering, S.I. / Rossjohn, J. / Reid, H.H. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8vcx.cif.gz | 413.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb8vcx.ent.gz | 280.8 KB | Display | PDB format |
| PDBx/mmJSON format | 8vcx.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8vcx_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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| Full document | 8vcx_full_validation.pdf.gz | 1.3 MB | Display | |
| Data in XML | 8vcx_validation.xml.gz | 30.2 KB | Display | |
| Data in CIF | 8vcx_validation.cif.gz | 41.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/8vcx ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vcx | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8vcyC ![]() 8vd0C ![]() 8vd2C ![]() 8vddC ![]() 8vduC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-T-CELL-RECEPTOR, ... , 2 types, 2 molecules DE
| #1: Protein | Mass: 22633.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: human islet-infiltrating CD4+ T cell clone isolated from the residual pancreatic islets from of a deceased organ donor who had T1D Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Gene: TRBV5-1*01 / Organ: Pancreas / Plasmid: pET30 / Production host: ![]() |
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| #2: Protein | Mass: 27076.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Gene: TRAV26-1*01 / Organ: Pancreas / Plasmid: pET30 / Production host: ![]() |
-MHC class II HLA-DQ- ... , 2 types, 2 molecules AB
| #3: Protein | Mass: 21150.596 Da / Num. of mol.: 1 / Mutation: C75I Source method: isolated from a genetically manipulated source Details: Class II histocompatibility antigen, alpha domain / Source: (gene. exp.) Homo sapiens (human) / Tissue: Skin, lymphoid, lungs, stomach and intestines / Cell: B Lymphocytes, dendritic cells, macrophages / Gene: HLA-DQA1 / Organ: Parenchyma / Plasmid: pZip3 / Cell (production host): cabbage looper ovarian / Cell line (production host): High Five (BTI-Tn-5B1-4) / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: Q30069 |
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| #4: Protein | Mass: 22605.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Skin, lymphoid, lungs, stomach and intestines / Cell: B Lymphocytes, dendritic cells, macrophages / Gene: HLA-DQB1 / Organ: Parenchyma / Plasmid: pZip3 / Cell (production host): cabbage looper ovarian / Cell line (production host): High Five (BTI-Tn-5B1-4) / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: O19707 |
-Protein/peptide , 1 types, 1 molecules C
| #5: Protein/peptide | Mass: 1388.461 Da / Num. of mol.: 1 / Mutation: G9E, L11C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Gene: INS / Organ: Pancreas / Plasmid: pZip3 / Cell (production host): cabbage looper ovarian / Cell line (production host): High Five (BTI-Tn-5B1-4) / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: P01308 |
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-Sugars , 2 types, 3 molecules
| #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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| #7: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 84 molecules 




| #8: Chemical | ChemComp-PO4 / | ||
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| #9: Chemical | ChemComp-GOL / #10: Water | ChemComp-HOH / | |
-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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| Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M Potassium sodium tartrate, 24% PEG 3350 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
| Reflection | Resolution: 2.59→45.53 Å / Num. obs: 34359 / % possible obs: 99.3 % / Redundancy: 13.6 % / Biso Wilson estimate: 63.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Net I/σ(I): 19.5 |
| Reflection shell | Resolution: 2.59→2.7 Å / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4028 / CC1/2: 0.923 / Rpim(I) all: 0.215 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→45.53 Å / SU ML: 0.3092 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1979 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 71.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.59→45.53 Å
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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 | Refine-ID: X-RAY DIFFRACTION
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Movie
Controller
About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
Australia, 2items
Citation




PDBj























Trichoplusia ni (cabbage looper)