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Open data
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Basic information
Entry | Database: PDB / ID: 5nmg | ||||||
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Title | 868 TCR in complex with HLA A02 presenting SLYFNTIAVL | ||||||
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Function / homology | ![]() host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / T cell mediated cytotoxicity directed against tumor cell target / Uncoating of the HIV Virion / 2-LTR circle formation ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / T cell mediated cytotoxicity directed against tumor cell target / Uncoating of the HIV Virion / 2-LTR circle formation / positive regulation of memory T cell activation / TAP complex binding / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Golgi medial cisterna / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Integration of provirus / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / APOBEC3G mediated resistance to HIV-1 infection / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / endoplasmic reticulum exit site / TAP binding / Binding and entry of HIV virion / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K. | ||||||
![]() | ![]() Title: Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope. Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. ...Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. / Beck, K. / Evavold, B.D. / Rizkallah, P.J. / Sewell, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 677.8 KB | Display | ![]() |
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PDB format | ![]() | 563.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nmdC ![]() 5nmeC ![]() 5nmfC ![]() 5nmhC ![]() 5nmkC ![]() 2bnuS ![]() 2v2wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules AFBG
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules CH
#3: Protein/peptide | ![]() Mass: 977.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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-Human T-cell ... , 2 types, 4 molecules DIEJ
#4: Protein | Mass: 22224.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #5: Protein | Mass: 27440.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 169 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-EDO / ![]() #7: Chemical | ![]() #8: Chemical | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.72→99.5 Å / Num. obs: 54939 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.72→2.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3990 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2BNU, 2V2W Resolution: 2.75→39.83 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.899 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.233 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→39.83 Å
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Refine LS restraints |
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