+Open data
-Basic information
Entry | Database: PDB / ID: 5w6a | ||||||
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Title | HLA-C*06:02 presenting ARTELYRSL | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / Antigen presentation / Human Leukocyte Antigen | ||||||
Function / homology | Function and homology information negative regulation of superoxide anion generation / leucine zipper domain binding / negative regulation of amyloid precursor protein biosynthetic process / embryonic cleavage / NRAGE signals death through JNK / regulation of mitotic cell cycle / negative regulation of apoptotic signaling pathway / negative regulation of reactive oxygen species metabolic process / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...negative regulation of superoxide anion generation / leucine zipper domain binding / negative regulation of amyloid precursor protein biosynthetic process / embryonic cleavage / NRAGE signals death through JNK / regulation of mitotic cell cycle / negative regulation of apoptotic signaling pathway / negative regulation of reactive oxygen species metabolic process / TAP binding / 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 / small-subunit processome / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / tau protein binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / ribosomal small subunit biogenesis / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / transcription regulator complex / amyloid fibril formation / adaptive immune response / learning or memory / cell adhesion / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / DNA damage response / Neutrophil degranulation / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Mobbs, J.I. / Vivian, J.P. / Rossjohn, J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. Authors: Mobbs, J.I. / Illing, P.T. / Dudek, N.L. / Brooks, A.G. / Baker, D.G. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w6a.cif.gz | 340.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w6a.ent.gz | 275.3 KB | Display | PDB format |
PDBx/mmJSON format | 5w6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6a ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6a | HTTPS FTP |
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-Related structure data
Related structure data | 5w67C 5w69C 4nt6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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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
#1: Protein | Mass: 32087.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q29963, UniProt: P10321*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1110.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9NY61*PLUS #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris propane pH 7.0, 0.1 M Na fluoride and 20 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→68.47 Å / Num. obs: 86176 / % possible obs: 99.6 % / Redundancy: 8.7 % / Rpim(I) all: 0.03 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4252 / Rpim(I) all: 0.32 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NT6 Resolution: 1.74→68.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.702 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.104 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.852 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→68.47 Å
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Refine LS restraints |
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