+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vh8 | ||||||
---|---|---|---|---|---|---|---|
Title | KIR3DL1 in complex with HLA-B*5701 | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor | ||||||
Function / homology | ![]() HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / natural killer cell mediated cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / TAP binding / FCGR activation / protection from natural killer cell mediated cytotoxicity / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / detection of bacterium / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / Regulation of Complement cascade / antigen binding / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / 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 / 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 / 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 / Regulation of actin dynamics for phagocytic cup formation / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / FCERI mediated NF-kB activation / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / 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 / Interferon gamma signaling / positive regulation of immune response / 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 / 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 / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vivian, J.P. / Rossjohn, J. | ||||||
![]() | ![]() Title: Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B Authors: Vivian, J.P. / Duncan, R.C. / Berry, R. / O'Connor, G.M. / Reid, H.H. / Beddoe, T. / Gras, S. / Saunders, P.M. / Olshina, M.A. / Widjaja, J.M.L. / Harpur, C.M. / Lin, J. / Maloveste, S.M. / ...Authors: Vivian, J.P. / Duncan, R.C. / Berry, R. / O'Connor, G.M. / Reid, H.H. / Beddoe, T. / Gras, S. / Saunders, P.M. / Olshina, M.A. / Widjaja, J.M.L. / Harpur, C.M. / Lin, J. / Maloveste, S.M. / Price, D.A. / Lafont, B.A.P. / McVicar, D.W. / Clements, C.S. / Brooks, A.G. / Rossjohn, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 314.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 249.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 3 types, 6 molecules ADBEGH
#1: Protein | Mass: 31639.059 Da / Num. of mol.: 2 / Fragment: HLA-B*5701, UNP residues 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 34927.266 Da / Num. of mol.: 2 / Fragment: KIR3DL1*001, UNP residues 22-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Protein/peptide / Sugars / Non-polymers , 3 types, 1594 molecules CF![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 966.109 Da / Num. of mol.: 2 / Fragment: UNP residues 93-101 / Source method: obtained synthetically / Details: synthesised peptide / Source: (synth.) ![]() #5: Sugar | ChemComp-NAG / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.47 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG 3350, 2% tacsimate pH 5.0, 0.1M tri-sodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 136837 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3 / % possible all: 87.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2RFX and 1IM9 Resolution: 1.8→35.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.88 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.97 / ESU R: 0.152 / ESU R Free: 0.135 / Phase error: 28.86 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.215 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.96 Å2 / Biso mean: 29.231 Å2 / Biso min: 10.62 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.85 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|