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Open data
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Basic information
Entry | Database: PDB / ID: 5t6z | ||||||
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Title | KIR3DL1 in complex with HLA-B*57:01-TW10 | ||||||
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![]() | IMMUNE SYSTEM / human leukocyte antigen Immunoglobulin domain antigen presentation | ||||||
Function / homology | ![]() HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / natural killer cell mediated cytotoxicity / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / natural killer cell mediated cytotoxicity / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / retroviral ribonuclease H / exoribonuclease H / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / DNA integration / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / viral genome integration into host DNA / RNA-directed DNA polymerase / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / viral penetration into host nucleus / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / symbiont-mediated suppression of host gene expression / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / host cell / positive regulation of T cell activation / Interferon alpha/beta signaling / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / DNA recombination / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / molecular adaptor activity / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / learning or memory Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pymm, P. / Rossjohn, J. / Vivian, J.P. | ||||||
![]() | ![]() Title: MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape. Authors: Pymm, P. / Illing, P.T. / Ramarathinam, S.H. / O'Connor, G.M. / Hughes, V.A. / Hitchen, C. / Price, D.A. / Ho, B.K. / McVicar, D.W. / Brooks, A.G. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.7 KB | Display | ![]() |
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PDB format | ![]() | 127.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5t6wC ![]() 5t6xC ![]() 5t6yC ![]() 5t70C ![]() 3vh8S C: citing same article ( S: Starting model for refinement |
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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
-Protein , 3 types, 3 molecules ABG
#1: Protein | Mass: 31736.172 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 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 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 33076.461 Da / Num. of mol.: 1 / Fragment: UNP residues 22-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein/peptide / Sugars / Non-polymers , 3 types, 655 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1162.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P03366*PLUS | ||
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#5: Sugar | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG 3350, 2% tacsimate pH 5.0 and 0.1M tri-sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.867 Å / Num. obs: 47511 / % possible obs: 94.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 11.2 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VH8 Resolution: 2→39.87 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.69
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 40.55 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→39.87 Å
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Refine LS restraints |
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LS refinement shell |
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