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- PDB-8gvg: The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Ne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gvg | ||||||
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Title | The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 (2F) peptide | ||||||
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Function / homology | ![]() 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway ...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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() HIV whole-genome vector AA1305#18 (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, G.F. / Shi, Y. / Ma, K. / Chai, Y. / Guan, J. / Qi, J. / Tan, S. / Dong, T. / Iwamoto, A. / Kawana-Tachikawa, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors. Authors: Ma, K. / Chai, Y. / Guan, J. / Tan, S. / Qi, J. / Kawana-Tachikawa, A. / Dong, T. / Iwamoto, A. / Shi, Y. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 396.3 KB | Display | ![]() |
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PDB format | ![]() | 291.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gvbC ![]() 8gviC ![]() 3vxmS S: Starting model for refinement 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
#1: Protein | Mass: 23132.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 28271.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 31683.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#4: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#5: Protein/peptide | Mass: 1024.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV whole-genome vector AA1305#18 (others) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.77 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium sulfate, 0.1 M Bis-Tris Propane (pH 7.5), 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.36→50 Å / Num. obs: 16829 / % possible obs: 98.9 % / Redundancy: 16.9 % / Biso Wilson estimate: 94.4 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 22.933 |
Reflection shell | Resolution: 3.36→3.48 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 5.539 / Num. unique obs: 16829 / Rsym value: 0.968 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3VXM Resolution: 3.37→40.94 Å / SU ML: 0.918 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 48.5006 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: 148.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.37→40.94 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 | Refine-ID: X-RAY DIFFRACTION
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