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- PDB-9oaj: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2 -

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Basic information

Entry
Database: PDB / ID: 9oaj
TitleAMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2
Components
  • Envelope glycoprotein gp120
  • Envelope glycoprotein gp41
  • T-cell surface glycoprotein CD4
KeywordsIMMUNE SYSTEM / HIV-1 Envelope glycoprotein / cluster of differentiation 4
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 speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsCui, J. / Lin, Z. / Du, J. / Pallesen, J.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T-cell surface glycoprotein CD4
B: Envelope glycoprotein gp41
A: Envelope glycoprotein gp120
D: T-cell surface glycoprotein CD4
E: Envelope glycoprotein gp41
F: Envelope glycoprotein gp120
G: T-cell surface glycoprotein CD4
H: Envelope glycoprotein gp41
I: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,65436
Polymers371,4629
Non-polymers7,19227
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 T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 51179.445 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Homo sapiens (human) / References: UniProt: P01730
#2: Protein Envelope glycoprotein gp41


Mass: 17428.814 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q1AII4
#3: Protein Envelope glycoprotein gp120


Mass: 55212.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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: AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2 / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337552 / Symmetry type: POINT

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