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Open data
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Basic information
Entry | Database: PDB / ID: 8vd2 | |||||||||
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Title | Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1 | |||||||||
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![]() | IMMUNE SYSTEM / Immune T cell receptor-pMHC II complex | |||||||||
Function / homology | ![]() antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tran, T.M. / Lim, J.J. / Loh, T.Y. / Mannering, I.S. / Rossjohn, J. / Reid, H.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 395.6 KB | Display | ![]() |
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PDB format | ![]() | 266.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.1 KB | Display | ![]() |
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Full document | ![]() | 486 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vcxC ![]() 8vcyC ![]() 8vd0C ![]() 8vddC ![]() 8vduC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-MHC class II HLA-DQ- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21150.596 Da / Num. of mol.: 1 / Mutation: I75C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 22605.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Class II histocompatibility antigen, alpha domain / Source: (gene. exp.) ![]() ![]() |
-T-CELL-RECEPTOR, TCR ET650-4 ... , 2 types, 2 molecules DE
#4: Protein | Mass: 22921.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Human CD4+ T cell clone isolated from PBMC of recent onset T1D patient Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 27153.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Human CD4+ T cell clone isolated from PBMC of recent onset T1D patient Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide / Sugars / Non-polymers , 3 types, 13 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1474.593 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A fusion of proinsulin C-peptide fragment and IAPP1 fragment Source: (gene. exp.) ![]() ![]() |
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#6: Sugar | ChemComp-NAG / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M potassium dihydrogen phosphate (KH2PO4), 15% w/v PEG 20,000 with seeding and additive 30 mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.9→49 Å / Num. obs: 20755 / % possible obs: 100 % / Redundancy: 3.1 % / Biso Wilson estimate: 58.91 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.096 / Rrim(I) all: 0.171 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.9→3.08 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3281 / CC1/2: 0.817 / Rpim(I) all: 0.4 / Rrim(I) all: 0.718 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 57.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 43.859894162 Å / Origin y: -19.748337874 Å / Origin z: -19.5718002526 Å
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Refinement TLS group | Selection details: all |