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Yorodumi- PDB-7f1t: Crystal structure of the human chemokine receptor CCR5 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f1t | |||||||||
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Title | Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a | |||||||||
Components | C-C motif chemokine 3,C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5 | |||||||||
Keywords | SIGNALING PROTEIN / G protein-coupled Receptor / Chemokine receptor CCR5 / MIP-1a | |||||||||
Function / homology | Function and homology information chemokine (C-C motif) ligand 5 binding / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / negative regulation of macrophage apoptotic process / signaling / astrocyte cell migration / chemokine receptor activity ...chemokine (C-C motif) ligand 5 binding / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / negative regulation of macrophage apoptotic process / signaling / astrocyte cell migration / chemokine receptor activity / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization / regulation of sensory perception of pain / C-C chemokine receptor activity / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / C-C chemokine binding / cell activation / phosphatidylinositol phospholipase C activity / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / dendritic cell chemotaxis / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / Binding and entry of HIV virion / cellular response to interleukin-1 / cellular defense response / coreceptor activity / positive regulation of calcium-mediated signaling / cytoskeleton organization / cell chemotaxis / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / intracellular calcium ion homeostasis / response to toxic substance / osteoblast differentiation / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of neuron apoptotic process / calcium ion transport / chemotaxis / MAPK cascade / positive regulation of tumor necrosis factor production / virus receptor activity / cell-cell signaling / cellular response to tumor necrosis factor / actin binding / kinase activity / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / G alpha (i) signalling events / cellular response to lipopolysaccharide / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / protein kinase activity / positive regulation of cell migration / immune response / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Clostridium pasteurianum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Zhang, H. / Chen, K. / Tan, Q. / Han, S. / Zhu, Y. / Zhao, Q. / Wu, B. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for chemokine recognition and receptor activation of chemokine receptor CCR5. Authors: Hui Zhang / Kun Chen / Qiuxiang Tan / Qiang Shao / Shuo Han / Chenhui Zhang / Cuiying Yi / Xiaojing Chu / Ya Zhu / Yechun Xu / Qiang Zhao / Beili Wu / Abstract: The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain ...The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain elusive. Here we report three cryo-electron microscopy structures of G protein-coupled CCR5 in a ligand-free state and in complex with the chemokine MIP-1α or RANTES, as well as the crystal structure of MIP-1α-bound CCR5. These structures reveal distinct binding modes of the two chemokines and a specific accommodate pattern of the chemokine for the distal N terminus of CCR5. Together with functional data, the structures demonstrate that chemokine-induced rearrangement of toggle switch and plasticity of the receptor extracellular region are critical for receptor activation, while a conserved tryptophan residue in helix II acts as a trigger of receptor constitutive activation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f1t.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f1t.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 7f1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/7f1t ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f1t | HTTPS FTP |
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-Related structure data
Related structure data | 7f1qC 7f1rC 7f1sC 4mbsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55445.453 Da / Num. of mol.: 1 Mutation: T15C,T108C,C150Y,M156A,G255N,A376D,R417A,T427A,K446E Source method: isolated from a genetically manipulated source Details: Fusion protein of MIP-1a and CCR5 from Homo sapiens, inserted with Rubredoxin from Clostridium pasteurianum Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria) Gene: CCL3, G0S19-1, MIP1A, SCYA3, CCR5, CMKBR5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P10147, UniProt: P51681, UniProt: P00268 |
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#2: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 64.24 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100mM HEPES, pH 6.0, 250mM ammonium sulfate, 30% (v/v) PEG 400, 8% (v/v) PPG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 18209 / % possible obs: 94.9 % / Redundancy: 6.7 % / CC1/2: 0.985 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Num. unique obs: 888 / CC1/2: 0.808 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MBS Resolution: 2.6→50 Å / Cross valid method: THROUGHOUT Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 117.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å
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