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- PDB-5uiw: Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uiw | |||||||||
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Title | Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5 | |||||||||
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![]() | SIGNALING PROTEIN / G-protein coupled receptor / Chemokine receptor / HIV entry inhibitor / HIV-1 R5 isolates co-receptor / receptor-ligand complex | |||||||||
Function / homology | ![]() regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / chemokine (C-C motif) ligand 5 binding / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / chemokine (C-C motif) ligand 5 binding / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / signaling / positive regulation of cell-cell adhesion mediated by integrin / chemokine receptor activity / positive regulation of activation of Janus kinase activity / alkane catabolic process / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / positive regulation of homotypic cell-cell adhesion / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / phosphatidylinositol phospholipase C activity / C-C chemokine receptor activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / C-C chemokine binding / neutrophil activation / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / negative regulation of viral genome replication / phospholipase activator activity / positive regulation of macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / regulation of insulin secretion / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of translational initiation / positive regulation of viral genome replication / Binding and entry of HIV virion / cellular response to interleukin-1 / cellular defense response / coreceptor activity / positive regulation of T cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / neutrophil chemotaxis / cell chemotaxis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / calcium-mediated signaling / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / response to toxic substance / cellular response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / chemotaxis / : / MAPK cascade / cell-cell signaling / virus receptor activity / cellular response to tumor necrosis factor / actin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / endosome / positive regulation of cell migration / inflammatory response / iron ion binding / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Zheng, Y. / Qin, L. / Han, G.W. / Gustavsson, M. / Kawamura, T. / Stevens, R.C. / Cherezov, V. / Kufareva, I. / Handel, T.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Authors: Zheng, Y. / Han, G.W. / Abagyan, R. / Wu, B. / Stevens, R.C. / Cherezov, V. / Kufareva, I. / Handel, T.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 | ![]() | 190.4 KB | Display | ![]() |
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PDB format | ![]() | 149.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mbsS 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 47158.828 Da / Num. of mol.: 1 / Mutation: C58Y, G163N, A233D, K303E Source method: isolated from a genetically manipulated source Details: Rubredoxin fusion sequence P00268; in between CCR5 residue 223 and 227 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE Source: (gene. exp.) ![]() ![]() Gene: CCR5, CMKBR5 / Plasmid: pfastbac-1 / Cell line (production host): sf9 / Organ (production host): Ovary / Production host: ![]() ![]() |
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#2: Protein | Mass: 8662.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence before CC motif "QGPPLMALQS" (where the first residue Q is PCA as glutamine is cyclized into pyroglutamic acid residue) is artificial to replace native sequence "SPYSSDTTP". As the ...Details: Sequence before CC motif "QGPPLMALQS" (where the first residue Q is PCA as glutamine is cyclized into pyroglutamic acid residue) is artificial to replace native sequence "SPYSSDTTP". As the register 0 for PCA, all the rest of residue numbers are consistent for chemokine residues. Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 53 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OLC.gif)
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![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | ChemComp-OLC / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.65 % |
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Crystal grow | Temperature: 295.5 K / Method: lipidic cubic phase / pH: 6.3 Details: 29% (v/v) PEG 400, 120 mM lithium citrate, 1.2% (w/v) 1,5-Diaminopentane dihydrochloride, 100 mM 2-(N-morpholino)ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2016 / Details: K-B pair of biomorph mirrors | |||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.18→29.472 Å / Num. obs: 32803 / % possible obs: 99.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.039 / Rrim(I) all: 0.151 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MBS Resolution: 2.204→29.472 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.87 Å2 / Biso mean: 42.3057 Å2 / Biso min: 5.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.204→29.472 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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