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Open data
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Basic information
Entry | Database: PDB / ID: 3vfp | ||||||
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Title | crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158 | ||||||
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Function / homology | ![]() symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / lumenal side of endoplasmic reticulum membrane / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Liu, Y.C. / Rossjohn, J. / Gras, S. | ||||||
![]() | ![]() Title: The Energetic Basis Underpinning T-cell Receptor Recognition of a Super-bulged Peptide Bound to a Major Histocompatibility Complex Class I Molecule. Authors: Liu, Y.C. / Chen, Z. / Burrows, S.R. / Purcell, A.W. / McCluskey, J. / Rossjohn, J. / Gras, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.2 KB | Display | ![]() |
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PDB format | ![]() | 78.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vfmC ![]() 3vfnC ![]() 3vfoC ![]() 3vfrC ![]() 3vfsC ![]() 3vftC ![]() 3vfuC ![]() 3vfvC ![]() 3vfwC ![]() 1zhkS 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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Unit cell |
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Components
#1: Protein | Mass: 31970.254 Da / Num. of mol.: 1 / Mutation: A182G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1426.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BL biochem / References: UniProt: P03206*PLUS |
#4: Chemical | ChemComp-ACT / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M ammonium acetate, 16% PEG 4K, 0.1M sodium citrate pH5.6, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Number: 249836 / Rmerge(I) obs: 0.079 / D res high: 1.7 Å / Num. obs: 36101 / % possible obs: 70.4 |
Diffraction reflection shell | Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / Num. obs: 3328 / % possible obs: 41.9 % / Rmerge(I) obs: 0.198 |
Reflection | Highest resolution: 1.7 Å / % possible obs: 70.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.003 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.55 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 8.12 / Num. measured obs: 24250 / Num. unique obs: 3328 / % possible all: 41.9 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1ZHK Resolution: 1.85→19.481 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.7983 / SU ML: 0.47 / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.99 Å2 / Biso mean: 21.1368 Å2 / Biso min: 6.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.481 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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