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- PDB-2x4q: Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavab... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x4q | ||||||||||||
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Title | Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavable peptide | ||||||||||||
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Function / homology | ![]() T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M. | ||||||||||||
![]() | ![]() Title: Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger. Authors: Rodenko, B. / Toebes, M. / Celie, P.H.N. / Perrakis, A. / Schumacher, T.N.M. / Ovaa, H. #1: ![]() Title: Uv-Induced Ligand Exchange in Mhc Class I Protein Crystals. Authors: Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.1 KB | Display | ![]() |
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PDB format | ![]() | 276.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x4pC ![]() 2x4tC ![]() 1eeyS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11973.146 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 CF
#3: Protein/peptide | Mass: 1195.225 Da / Num. of mol.: 2 / Fragment: FRAGMENT RESIDUES 58-66 / Source method: obtained synthetically Details: MODIFIED AT P5 (RESIDUE62) AND P8 (RESIDUE 65).(2-NITRO)PHENYL-PROPIONIC ACID AT P5 AND 3-AMINO-3-(2- NITRO)PHENYL-PROPIONIC ACID AT P8 Source: (synth.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 316 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
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#4: Chemical | ![]() #5: Chemical | ChemComp-GOL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | INITIALIZING METHIONINE (B0 AND E0) ADDED TO SEQUENCE ORIGINAL SEQUENCE IS GILGFVFTL. G AT P1 IS ...INITIALIZI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 44.9 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: 0.1M MES PH 6.5, 20% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 8, 2007 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection twin | Operator: -h,-k,l / Fraction: 0.337 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 64908 / % possible obs: 97.2 % / Observed criterion σ(I): -3.7 / Redundancy: 3.4 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.1 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1EEY Resolution: 1.9→32.434 Å / σ(F): 1.38 / Phase error: 38.52 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.283 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.434 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 |
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