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- EMDB-48215: Global structure of hCXCR4 and HIV-2 gp120 -

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Basic information

Entry
Database: EMDB / ID: EMD-48215
TitleGlobal structure of hCXCR4 and HIV-2 gp120
Map dataGlobal halfA map of hCXCR4 and HIV-2 gp120 complex
Sample
  • Complex: Global structure of hCXCR4-HIV2_gp120 complex
    • Protein or peptide: C-X-C chemokine receptor type 4
    • Protein or peptide: gp120
KeywordsHIV-2 / gp120 / CXCR4 / receptor / SIGNALING PROTEIN
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 / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / C-X-C chemokine receptor activity / positive regulation of vasculature development / Signaling by ROBO receptors ...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 / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / C-X-C chemokine receptor activity / positive regulation of vasculature development / Signaling by ROBO receptors / Formation of definitive endoderm / C-C chemokine receptor activity / membrane fusion involved in viral entry into host cell / C-C chemokine binding / anchoring junction / Chemokine receptors bind chemokines / dendritic cell chemotaxis / cellular response to cytokine stimulus / cell leading edge / positive regulation of oligodendrocyte differentiation / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / neurogenesis / host cell endosome membrane / cell chemotaxis / ubiquitin binding / calcium-mediated signaling / brain development / G protein-coupled receptor activity / response to virus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / late endosome / positive regulation of cold-induced thermogenesis / virus receptor activity / positive regulation of cytosolic calcium ion concentration / actin binding / cytoplasmic vesicle / G alpha (i) signalling events / early endosome / response to hypoxia / lysosome / positive regulation of cell migration / immune response / G protein-coupled receptor signaling pathway / inflammatory response / external side of plasma membrane / apoptotic process / viral envelope / ubiquitin protein ligase binding / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / protein-containing complex / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Chemokine receptor family / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Chemokine receptor family / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Envelope glycoprotein gp160 / C-X-C chemokine receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsZhang Z / Patel DJ
Funding support United States, 1 items
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 6, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48215.png

Downloads & links

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Map

FileDownload / File: emd_48215.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal halfA map of hCXCR4 and HIV-2 gp120 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 420 pix.
= 304.5 Å		0.73 Å/pix.
x 420 pix.
= 304.5 Å		0.73 Å/pix.
x 420 pix.
= 304.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.36984614 - 0.70288944
Average (Standard dev.)0.0018043406 (±0.02210389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 304.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Global halfA map of hCXCR4 and HIV-2 gp120 complex

Fileemd_48215_half_map_1.map
AnnotationGlobal halfA map of hCXCR4 and HIV-2 gp120 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Global halfB map of hCXCR4 and HIV-2 gp120 complex

Fileemd_48215_half_map_2.map
AnnotationGlobal halfB map of hCXCR4 and HIV-2 gp120 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Global structure of hCXCR4-HIV2_gp120 complex

EntireName: Global structure of hCXCR4-HIV2_gp120 complex
Components
  • Complex: Global structure of hCXCR4-HIV2_gp120 complex
    • Protein or peptide: C-X-C chemokine receptor type 4
    • Protein or peptide: gp120

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Supramolecule #1: Global structure of hCXCR4-HIV2_gp120 complex

SupramoleculeName: Global structure of hCXCR4-HIV2_gp120 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C-X-C chemokine receptor type 4

MacromoleculeName: C-X-C chemokine receptor type 4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.784359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGISIYTSD NYTEEMGSGD YDSMKEPCFR EENANFNKIF LPTIYSIIFL TGIVGNGLVI LVMGYQKKLR SMTDKYRLHL SVADLLFVI TLPFWAVDAV ANWYFGNFLC KAVHVIYTVN LYSSVLILAF ISLDRYLAIV HATNSQRPRK LLAEKVVYVG V WIPALLLT ...String:
MEGISIYTSD NYTEEMGSGD YDSMKEPCFR EENANFNKIF LPTIYSIIFL TGIVGNGLVI LVMGYQKKLR SMTDKYRLHL SVADLLFVI TLPFWAVDAV ANWYFGNFLC KAVHVIYTVN LYSSVLILAF ISLDRYLAIV HATNSQRPRK LLAEKVVYVG V WIPALLLT IPDFIFANVS EADDRYICDR FYPNDLWVVV FQFQHIMVGL ILPGIVILSC YCIIISKLSH SKGHQKRKAL KT TVILILA FFACWLPYYI GISIDSFILL EIIKQGCEFE NTVHKWISIT EALAFFHCCL NPILYAFLGA KFKTSAQHAL TSV SRGSSL KILSKGKRGG HSSVSTESES SSFHSSDYKD DDDK

UniProtKB: C-X-C chemokine receptor type 4

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Macromolecule #2: gp120

MacromoleculeName: gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 55.289422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KQFVTVFYGI PAWRNASIPL FCATKNRDTW GTIQCLPDND DYQEIALNVT EAFDAWNNTV TEQAVEDVWN LFETSIKPCV KLTPLCVAM NCTRNMTTST GTTDTQNITI INDTSPCVRA DNCTGLKEEE MVDCQFNMTG LERDKRKQYT EAWYSKDVIC D NNTSSRSK ...String:
KQFVTVFYGI PAWRNASIPL FCATKNRDTW GTIQCLPDND DYQEIALNVT EAFDAWNNTV TEQAVEDVWN LFETSIKPCV KLTPLCVAM NCTRNMTTST GTTDTQNITI INDTSPCVRA DNCTGLKEEE MVDCQFNMTG LERDKRKQYT EAWYSKDVIC D NNTSSRSK CYMNHCNTSV ITESCDKHYW DAMRFRYCAP PGFALLRCND TNYSGFAPNC SKVVAATCTR MMETQSSTWF GF NGTRAEN RTYIYWHGKN NRTIISLNNF YNLTMHCKRP GNKTVLPIMS GFKFHSKPVI NKKPRQAWCW FKGEWKEAMQ EVK ETLAKH PRYKGNRSRT ENIKFKAPGR GSDPEAAYMW TNCRGEFLYC NMTWFLNWVD NRTGQKQRNY APCHIRQIIN TWHR VGKNV YLPPREGELT CNSTVTSIIA NIDTGDQTDI TFSAEVAELY RLELGDYKLV EITPIGFAPT SVKRYSSAHQ RHTR

UniProtKB: Envelope glycoprotein gp160

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Alphafold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38914
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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