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- PDB-7f1t: Crystal structure of the human chemokine receptor CCR5 in complex... -

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Basic information

Entry
Database: PDB / ID: 7f1t
TitleCrystal structure of the human chemokine receptor CCR5 in complex with MIP-1a
ComponentsC-C motif chemokine 3,C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
KeywordsSIGNALING PROTEIN / G protein-coupled Receptor / Chemokine receptor CCR5 / MIP-1a
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / regulation of behavior / astrocyte cell migration / alkane catabolic process ...chemokine (C-C motif) ligand 5 binding / lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / regulation of behavior / astrocyte cell migration / alkane catabolic process / chemokine receptor activity / CCR5 chemokine receptor binding / eosinophil degranulation / CCR chemokine receptor binding / regulation of sensory perception of pain / signaling / negative regulation of bone mineralization / positive regulation of microglial cell activation / cell activation / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine receptor activity / T cell chemotaxis / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / response to cholesterol / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / phospholipase activator activity / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / exocytosis / cellular response to interleukin-1 / host-mediated suppression of viral transcription / Binding and entry of HIV virion / cellular defense response / coreceptor activity / neutrophil chemotaxis / cytoskeleton organization / positive regulation of calcium-mediated signaling / positive regulation of interleukin-1 beta production / cell chemotaxis / calcium-mediated signaling / cellular response to type II interferon / response to toxic substance / intracellular calcium ion homeostasis / chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / osteoblast differentiation / cellular response to tumor necrosis factor / calcium ion transport / kinase activity / cell-cell signaling / positive regulation of neuron apoptotic process / MAPK cascade / regulation of cell shape / actin binding / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / virus receptor activity / G alpha (i) signalling events / electron transfer activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / endosome / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / iron ion binding / inflammatory response / negative regulation of gene expression / external side of plasma membrane / apoptotic process / positive regulation of gene expression / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Rubredoxin-like domain ...CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Rubredoxin-like domain / Rubredoxin-like domain profile. / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rubredoxin / C-C motif chemokine 3 / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, H. / Chen, K. / Tan, Q. / Han, S. / Zhu, Y. / Zhao, Q. / Wu, B.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730027 China
National Natural Science Foundation of China (NSFC)31825010 China
CitationJournal: 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
DepositionJun 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 3,C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5112
Polymers55,4451
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.133, 204.356, 69.012
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein C-C motif chemokine 3,C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5 / G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT ...G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT 464.1 / SIS-beta / Small-inducible cytokine A3 / Tonsillar lymphocyte LD78 alpha protein / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor / Rd


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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.6→2.64 Å / Num. unique obs: 888 / CC1/2: 0.808

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Processing

Software
NameVersionClassification
BUSTERv.2.8.0refinement
HKL-2000v717data reduction
HKL-2000v717data scaling
PHASER1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS

4mbs


Resolution: 2.6→50 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.271 884 -
Rwork0.228 --
obs-17242 94.9 %
Displacement parametersBiso mean: 117.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 1 0 3372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01253463
X-RAY DIFFRACTIONf_angle_d1.70944722
X-RAY DIFFRACTIONf_chiral_restr0.0809541
X-RAY DIFFRACTIONf_plane_restr0.009589
X-RAY DIFFRACTIONf_dihedral_angle_d11.67591203
LS refinement shellResolution: 2.6→2.64 Å
RfactorNum. reflection% reflection
Rfree0.3494 55 -
Rwork0.306 1040 -
obs--75.6 %

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