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- EMDB-70287: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2 -

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Basic information

Entry
Database: EMDB / ID: EMD-70287
TitleAMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2
Map dataAMC008 SOSIP.v.4.2 in complex with CD4 D1D2
Sample
  • Complex: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2
    • Protein or peptide: T-cell surface glycoprotein CD4
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Envelope glycoprotein / cluster of differentiation 4 / IMMUNE SYSTEM
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / MHC class II protein binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / MHC class II protein binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / response to vitamin D / 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 / positive regulation of protein kinase activity / regulation of calcium ion transport / positive regulation of calcium ion transport into cytosol / macrophage differentiation / Generation of second messenger molecules / immunoglobulin binding / T cell differentiation / Co-inhibition by PD-1 / Binding and entry of HIV virion / coreceptor activity / positive regulation of T cell proliferation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / positive regulation of protein phosphorylation / MHC class II protein complex binding / transmembrane signaling receptor activity / response to estradiol / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / virus receptor activity / response to ethanol / host cell endosome / defense response to Gram-negative bacterium / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / early endosome / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / positive regulation of MAPK cascade / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / lipid binding / protein kinase binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 / Immunoglobulin / Immunoglobulin domain / Retroviral envelope protein ...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 / Immunoglobulin / Immunoglobulin domain / Retroviral envelope protein / Retroviral envelope protein GP41-like / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / 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 / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsCui J / Lin Z / Du J / Pallesen J
Funding support United States, 2 items
OrganizationGrant numberCountry
Other privateW.W.Smith Charitable Trust #A2404 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI166916-01A1 United States
CitationJournal: To Be Published
Title: Conformational Landscape of HIV-1 Env from Closed to Fully Open
Authors: Cui J / Lin Z / Du J / Pallesen J
History
DepositionApr 21, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70287.png

Downloads & links

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Map

FileDownload / File: emd_70287.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC008 SOSIP.v.4.2 in complex with CD4 D1D2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 379.44 Å		1.05 Å/pix.
x 360 pix.
= 379.44 Å		1.05 Å/pix.
x 360 pix.
= 379.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.0560687 - 4.770676
Average (Standard dev.)0.00041580712 (±0.05725092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 379.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of AMC008 SOSIP.v.4.2 in complex with...

Fileemd_70287_additional_1.map
AnnotationUnsharpened map of AMC008 SOSIP.v.4.2 in complex with CD4 D1D2 from classification focused on Env apex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of AMC008 SOSIP.v.4.2 in complex with CD4 D1D2

Fileemd_70287_half_map_1.map
AnnotationHalf map of AMC008 SOSIP.v.4.2 in complex with CD4 D1D2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of AMC008 SOSIP.v.4.2 in complex with CD4 D1D2

Fileemd_70287_half_map_2.map
AnnotationHalf map of AMC008 SOSIP.v.4.2 in complex with CD4 D1D2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2

EntireName: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2
Components
  • Complex: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2
    • Protein or peptide: T-cell surface glycoprotein CD4
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2

SupramoleculeName: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.179445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNRGVPFRHL LLVLQLALLP AATQGKKVVL GKKGDTVELT CTASQKKSIQ FHWKNSNQIK ILGNQGSFLT KGPSKLNDRA DSRRSLWDQ GNFPLIIKNL KIEDSDTYIC EVEDQKEEVQ LLVFGLTANS DTHLLQGQSL TLTLESPPGS SPSVQCRSPR G KNIQGGKT ...String:
MNRGVPFRHL LLVLQLALLP AATQGKKVVL GKKGDTVELT CTASQKKSIQ FHWKNSNQIK ILGNQGSFLT KGPSKLNDRA DSRRSLWDQ GNFPLIIKNL KIEDSDTYIC EVEDQKEEVQ LLVFGLTANS DTHLLQGQSL TLTLESPPGS SPSVQCRSPR G KNIQGGKT LSVSQLELQD SGTWTCTVLQ NQKKVEFKID IVVLAFQKAS SIVYKKEGEQ VEFSFPLAFT VEKLTGSGEL WW QAERASS SKSWITFDLK NKEVSVKRVT QDPKLQMGKK LPLHLTLPQA LPQYAGSGNL TLALEAKTGK LHQEVNLVVM RAT QLQKNL TCEVWGPTSP KLMLSLKLEN KEAKVSKREK AVWVLNPEAG MWQCLLSDSG QVLLESNIKV LPTWSTPVQP MALI VLGGV AGLLLFIGLG IFFCVRCRHR RRQAERMSQI KRLLSEKKTC QCPHRFQKTC SPI

UniProtKB: T-cell surface glycoprotein CD4

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Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.428814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGTIGAMFL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQNNLLRAPE AQQHLLQLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCS GKLICCTSVP WNTSWSNKSL DKIWNNMTWM EWEREIDNYT SLIYTLLEES QNQQEKNEQE LLELD

UniProtKB: Env polyprotein

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Macromolecule #3: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 55.212527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWTWILFLV AAATRVHSTE KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVRNVWATH ACVPTDPSPQ EVILENVTEN FNMWTNNMV EQMHEDIISL WDQSLKPCVK LTPLCVTLNC TNELKNTTKT NNSSWGGEMK NCSFNVTTSI RDKVQKEYAL F YKLDIVPI ...String:
MDWTWILFLV AAATRVHSTE KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVRNVWATH ACVPTDPSPQ EVILENVTEN FNMWTNNMV EQMHEDIISL WDQSLKPCVK LTPLCVTLNC TNELKNTTKT NNSSWGGEMK NCSFNVTTSI RDKVQKEYAL F YKLDIVPI DDDNNTSNYR LINCNTSVIT QACPKITFEP IPIQFCTPAG FAILKCNNKK FNGKGPCTNV STVQCTHGIR PV VSTQLLL NGSLAEEEVI IRSDNFTDNA KTIIVQLNES VVINCTRPNN NTRKSINIGP GRWFYTTGEI IGDIRQAHCN LSR TQWNNT LKQIAIKLRE QFENKTIVFN QSSGGDPEIV MHSFNCGGEF FYCNTTKLFN STWNDTDIRG NNTEGNDTIT IPCR IKQIV NMWQEVGKAM YAPPIRGQIR CSSNITGLLL TRDGGSESNT TEIFRPGGGD MRDNWRSELY KYKVVRIEPL GVAPT KCKR RVVQ

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 21 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 337552
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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