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- EMDB-48219: CXCR4-HIV-2/gp120-CD4 -

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Basic information

Entry
Database: EMDB / ID: EMD-48219
TitleCXCR4-HIV-2/gp120-CD4
Map datacryo-EM density map of CXCR4 bound to HIV-2/gp120-CD4 complex
Sample
  • Complex: cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex
    • Protein or peptide: C-X-C chemokine receptor type 4
    • Protein or peptide: T-cell surface glycoprotein CD4
    • Protein or peptide: HIV-1/gp120
Keywordscxcr4 / HIV-2 gp120 / CD4 / D1-D2 / 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 / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / myelin maintenance ...C-X-C motif chemokine 12 receptor activity / positive regulation of macrophage migration inhibitory factor signaling pathway / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / myelin maintenance / C-X-C chemokine receptor activity / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / positive regulation of vasculature development / Signaling by ROBO receptors / MHC class II protein binding / regulation of chemotaxis / Formation of definitive endoderm / C-C chemokine receptor activity / positive regulation of kinase activity / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / Developmental Lineage of Pancreatic Acinar Cells / C-C chemokine binding / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / response to vitamin D / Chemokine receptors bind chemokines / anchoring junction / dendritic cell chemotaxis / extracellular matrix structural constituent / Other interleukin signaling / T cell receptor complex / 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 calcium ion transport into cytosol / positive regulation of protein kinase activity / regulation of calcium ion transport / positive regulation of oligodendrocyte differentiation / Generation of second messenger molecules / macrophage differentiation / immunoglobulin binding / T cell differentiation / Co-inhibition by PD-1 / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / neurogenesis / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / Vpu mediated degradation of CD4 / ubiquitin binding / cell chemotaxis / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / G protein-coupled receptor activity / brain development / response to virus / positive regulation of protein phosphorylation / MHC class II protein complex binding / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / transmembrane signaling receptor activity / Clathrin-mediated endocytosis / late endosome / response to estradiol / signaling receptor activity / positive regulation of cold-induced thermogenesis / actin binding / positive regulation of cytosolic calcium ion concentration / virus receptor activity / cytoplasmic vesicle / response to ethanol / G alpha (i) signalling events / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of viral entry into host cell / early endosome / response to hypoxia / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / positive regulation of MAPK cascade / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / membrane raft / endoplasmic reticulum lumen
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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin subtype / 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 speciesCronobacter phage ES2 (virus) / Homo sapiens (human) / Virus-associated RNAs
Methodsingle particle reconstruction / cryo EM / Resolution: 5.65 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: To Be Published
Title: Structure of CXCR4-HIV-2/gp120-CD4 complex.
Authors: Zhang Z / Patel DJ
History
DepositionDec 8, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48219.png

Downloads & links

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Map

FileDownload / File: emd_48219.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM density map of CXCR4 bound to HIV-2/gp120-CD4 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: 0.06
Minimum - Maximum-0.27825853 - 0.5591555
Average (Standard dev.)-0.000005426938 (±0.02060044)
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: cryo-EM half B density map of CXCR4 bound to HIV-2/gp120-CD4 complex.

Fileemd_48219_half_map_1.map
Annotationcryo-EM half B density map of CXCR4 bound to HIV-2/gp120-CD4 complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half A density map of CXCR4 bound to HIV-2/gp120-CD4 complex

Fileemd_48219_half_map_2.map
Annotationcryo-EM half A density map of CXCR4 bound to HIV-2/gp120-CD4 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 : cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex

EntireName: cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex
Components
  • Complex: cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex
    • Protein or peptide: C-X-C chemokine receptor type 4
    • Protein or peptide: T-cell surface glycoprotein CD4
    • Protein or peptide: HIV-1/gp120

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Supramolecule #1: cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex

SupramoleculeName: cryoEM structure of CXCR4-HIV-2/gp120-CD4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cronobacter phage ES2 (virus)

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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: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.541176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KKVVLGKKGD TVELTCTASQ KKSIQFHWKN SNQIKILGNQ GSFLTKGPSK LNDRADSRRS LWDQGNFPLI IKNLKIEDSD TYICEVEDQ KEEVQLLVFG LTANSDTHLL QGQSLTLTLE SPPGSSPSVQ CRSPRGKNIQ GGKTLSVSQL ELQDSGTWTC T VLQNQKKV EFKIDIVV

UniProtKB: T-cell surface glycoprotein CD4

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Macromolecule #3: HIV-1/gp120

MacromoleculeName: HIV-1/gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Virus-associated RNAs
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

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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: 60.3 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphaflod2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41735
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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