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- PDB-9met: CXCR4-HIV-2/gp120-CD4 -

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Basic information

Entry
Database: PDB / ID: 9met
TitleCXCR4-HIV-2/gp120-CD4
Components
  • C-X-C chemokine receptor type 4
  • HIV-1/gp120
  • T-cell surface glycoprotein CD4
KeywordsSIGNALING PROTEIN / cxcr4 / HIV-2 gp120 / CD4 / D1-D2
Function / homology
Function and homology information


C-X-C motif chemokine 12 receptor activity / positive regulation of macrophage migration inhibitory factor signaling pathway / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway / Specification of primordial germ cells / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells ...C-X-C motif chemokine 12 receptor activity / positive regulation of macrophage migration inhibitory factor signaling pathway / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway / Specification of primordial germ cells / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / C-X-C chemokine receptor activity / maintenance of protein location in cell / response to methamphetamine hydrochloride / cellular response to ionomycin / positive regulation of vasculature development / T cell selection / Signaling by ROBO receptors / MHC class II protein binding / Formation of definitive endoderm / C-C chemokine receptor activity / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / C-C chemokine binding / positive regulation of monocyte differentiation / Alpha-defensins / Nef Mediated CD4 Down-regulation / anchoring junction / regulation of T cell activation / response to vitamin D / Chemokine receptors bind chemokines / dendritic cell chemotaxis / Other interleukin signaling / T cell receptor complex / extracellular matrix structural constituent / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cellular response to cytokine stimulus / cell leading edge / positive regulation of oligodendrocyte differentiation / Generation of second messenger molecules / macrophage differentiation / immunoglobulin binding / T cell differentiation / Co-inhibition by PD-1 / positive regulation of calcium ion transport into cytosol / Binding and entry of HIV virion / regulation of cell adhesion / positive regulation of interleukin-2 production / coreceptor activity / positive regulation of T cell proliferation / positive regulation of calcium-mediated signaling / neurogenesis / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / cell chemotaxis / ubiquitin binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / brain development / G protein-coupled receptor activity / response to virus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / MHC class II protein complex binding / late endosome / transmembrane signaling receptor activity / response to estradiol / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / positive regulation of cold-induced thermogenesis / Clathrin-mediated endocytosis / virus receptor activity / positive regulation of cytosolic calcium ion concentration / signaling receptor activity / actin binding / cytoplasmic vesicle / G alpha (i) signalling events / defense response to Gram-negative bacterium / response to ethanol / adaptive immune response / early endosome / response to hypoxia / lysosome / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / immune response / membrane raft / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / symbiont entry into host cell / lipid binding / endoplasmic reticulum membrane / protein kinase binding
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Chemokine receptor family / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / Immunoglobulin subtype / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / C-X-C chemokine receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Virus-associated RNAs
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.65 Å
AuthorsZhang, Z. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
CitationJournal: Nat Commun / Year: 2025
Title: CXCR4 mediated recognition of HIV envelope spike and inhibition by CXCL12.
Authors: Zhiying Zhang / Hongwei Zhang / Lyuqin Zheng / Shihua Chen / Shuo Du / Junyu Xiao / Dinshaw J Patel /
Abstract: CCR5 and CXCR4 both act as HIV co-receptors, though CXCR4 is less explored. CXCR4 binds the chemokine CXCL12 to regulate cellular processes and mediate HIV entry, a process that CXCL12 inhibits. ...CCR5 and CXCR4 both act as HIV co-receptors, though CXCR4 is less explored. CXCR4 binds the chemokine CXCL12 to regulate cellular processes and mediate HIV entry, a process that CXCL12 inhibits. Using cryo-EM, we investigate HIV-2 envelope (Env) spike recognition by CXCR4 and how CXCL12 inhibit this interaction. We discover that CXCR4 unexpected forms a tetramer, both alone and in complex. It binds CXCL12 with 4:8 and 8:8 stoichiometries, with the CXCL12 N-terminus inserting into the CXCR4 pocket. Structures of CXCR4-gp120 complex show one or two gp120 molecules per CXCR4 tetramer, with the V3 loop occupying the major sub-pocket of CXCR4 through deep embedment of its GFKF motif. The CXCL12 N-terminus chashes with gp120 V3 loops, explain its inhibitory effect. Docking analyses of other HIV antagonists further clarify their mechanisms. The CXCR4-gp120 model illustrate how V3 loop residues define co-receptor specificity, offering insights into co-receptor switching and therapeutic design.
History
DepositionDec 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: C-X-C chemokine receptor type 4
N: C-X-C chemokine receptor type 4
O: C-X-C chemokine receptor type 4
S: C-X-C chemokine receptor type 4
R: T-cell surface glycoprotein CD4
T: HIV-1/gp120
A: T-cell surface glycoprotein CD4
Q: HIV-1/gp120


Theoretical massNumber of molelcules
Total (without water)312,7998
Polymers312,7998
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
C-X-C chemokine receptor type 4 / CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain ...CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain receptor / LESTR / Lipopolysaccharide-associated protein 3 / LAP-3 / LPS-associated protein 3 / NPYRL / Stromal cell-derived factor 1 receptor / SDF-1 receptor


Mass: 40784.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR4 / Production host: Homo sapiens (human) / References: UniProt: P61073
#2: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 19541.176 Da / Num. of mol.: 2
Fragment: Ig-like V-type and Ig-like C2-type 1 domains (UNP residues 26-201)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Homo sapiens (human) / References: UniProt: P01730
#3: Protein HIV-1/gp120


Mass: 55289.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Virus-associated RNAs / Production host: Homo sapiens (human)
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: cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Cronobacter phage ES2 (virus)
Source (recombinant)Organism: Homo sapiens (human)
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41735 / Symmetry type: POINT
RefinementHighest resolution: 5.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01119552
ELECTRON MICROSCOPYf_angle_d1.27426560
ELECTRON MICROSCOPYf_dihedral_angle_d5.4182554
ELECTRON MICROSCOPYf_chiral_restr0.0643004
ELECTRON MICROSCOPYf_plane_restr0.0083318

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