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- PDB-7f1r: Cryo-EM structure of the chemokine receptor CCR5 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f1r
TitleCryo-EM structure of the chemokine receptor CCR5 in complex with RANTES and Gi
Components
  • C-C motif chemokine 5,C-C chemokine receptor type 5
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / Chemokine receptor CCR5 / RANTES
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / activation of phospholipase D activity / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / : / 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 / activation of phospholipase D activity / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / : / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / signaling / cell surface receptor signaling pathway via STAT / chemokine receptor activity / positive regulation of cell-cell adhesion mediated by integrin / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / positive regulation of homotypic cell-cell adhesion / CCR chemokine receptor binding / C-C chemokine receptor activity / neutrophil activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of T cell apoptotic process / C-C chemokine binding / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / regulation of T cell activation / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / positive regulation of innate immune response / positive regulation of monocyte chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of viral genome replication / leukocyte cell-cell adhesion / phospholipase activator activity / positive regulation of macrophage chemotaxis / macrophage chemotaxis / positive regulation of smooth muscle cell migration / chemoattractant activity / monocyte chemotaxis / Interleukin-10 signaling / exocytosis / cellular response to interleukin-1 / negative regulation by host of viral transcription / T cell migration / positive regulation of T cell migration / D2 dopamine receptor binding / Binding and entry of HIV virion / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / positive regulation of translational initiation / cellular defense response / positive regulation of viral genome replication / regulation of cAMP-mediated signaling / coreceptor activity / G protein-coupled serotonin receptor binding / positive regulation of T cell proliferation / positive regulation of phosphorylation / cellular response to forskolin / positive regulation of tyrosine phosphorylation of STAT protein / regulation of mitotic spindle organization / regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of cell adhesion / positive regulation of epithelial cell proliferation / cell chemotaxis / epithelial cell proliferation / Regulation of insulin secretion / G protein-coupled receptor binding / positive regulation of smooth muscle cell proliferation / calcium-mediated signaling / response to virus / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / cellular response to virus / cellular response to type II interferon / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / response to peptide hormone / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / response to toxic substance / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste
Similarity search - Function
CC chemokine receptor 5 / Chemokine receptor family / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / : / 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 ...CC chemokine receptor 5 / Chemokine receptor family / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / : / 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 / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
C-C motif chemokine 5 / C-C chemokine receptor type 5 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
R: C-C motif chemokine 5,C-C chemokine receptor type 5
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2


Theoretical massNumber of molelcules
Total (without water)137,8264
Polymers137,8264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein C-C motif chemokine 5,C-C chemokine receptor type 5 / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 52101.227 Da / Num. of mol.: 1 / Mutation: F28C,G258N,E267C
Source method: isolated from a genetically manipulated source
Details: Fusion protein of RANTES and CCR5 / Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5, CCR5, CMKBR5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13501, UniProt: P51681
#2: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40447.141 Da / Num. of mol.: 1 / Mutation: S47C,G202T,G203A,E245A,A326S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63096
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chemokine receptor CCR5 in complex with RANTES and Gi / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.1875 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1304062 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00186762
ELECTRON MICROSCOPYf_angle_d0.47459206
ELECTRON MICROSCOPYf_chiral_restr0.03781098
ELECTRON MICROSCOPYf_plane_restr0.00311148
ELECTRON MICROSCOPYf_dihedral_angle_d17.58352243

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