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- PDB-3j70: Model of gp120, including variable regions, in complex with CD4 a... -

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Basic information

Entry
Database: PDB / ID: 3j70
TitleModel of gp120, including variable regions, in complex with CD4 and 17b
Components
  • Envelope glycoprotein gp120
  • T-cell surface glycoprotein CD4
  • envelope glycoprotein gp41
  • monoclonal antibody 17b heavy chain
  • monoclonal antibody 17b light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / gp120 / V1V2 / CD4 / 17b / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / cellular response to ionomycin / maintenance of protein location in cell / response to methamphetamine hydrochloride / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / cellular response to ionomycin / maintenance of protein location in cell / response to methamphetamine hydrochloride / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / symbiont-mediated evasion of host immune response / interleukin-15-mediated signaling pathway / positive regulation of establishment of T cell polarity / regulation of T cell activation / positive regulation of monocyte differentiation / response to vitamin D / Alpha-defensins / Nef Mediated CD4 Down-regulation / T cell receptor complex / leukocyte chemotaxis / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / extracellular matrix structural constituent / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / macrophage differentiation / Generation of second messenger molecules / positive regulation of calcium ion transport into cytosol / T cell differentiation / Co-inhibition by PD-1 / Binding and entry of HIV virion / immunoglobulin binding / coreceptor activity / positive regulation of plasma membrane raft polarization / positive regulation of interleukin-2 production / positive regulation of receptor clustering / positive regulation of T cell proliferation / actin filament organization / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / host cell endosome membrane / T cell activation / virus receptor activity / clathrin-coated endocytic vesicle membrane / Vpu mediated degradation of CD4 / Assembly Of The HIV Virion / Budding and maturation of HIV virion / T cell receptor signaling pathway / positive regulation of inflammatory response / response to estradiol / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / cell adhesion / clathrin-dependent endocytosis of virus by host cell / early endosome / response to ethanol / cell surface receptor signaling pathway / viral protein processing / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / signaling receptor binding / lipid binding / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / protein kinase binding / virion attachment to host cell / endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / structural molecule activity / signal transduction / enzyme binding / protein homodimerization activity / zinc ion binding / membrane / identical protein binding / 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 / Envelope glycoprotein Gp160 ...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 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin subtype 2 / Immunoglobulin C-2 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsRasheed, M. / Bettadapura, R. / Bajaj, C.
CitationJournal: Nature / Year: 2008
Title: Molecular architecture of native HIV-1 gp120 trimers.
Authors: Jun Liu / Alberto Bartesaghi / Mario J Borgnia / Guillermo Sapiro / Sriram Subramaniam /
Abstract: The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. ...The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms trimers on the surface of the viral membrane. Using cryo-electron tomography combined with three-dimensional image classification and averaging, we report the three-dimensional structures of trimeric Env displayed on native HIV-1 in the unliganded state, in complex with the broadly neutralizing antibody b12 and in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal structures of the monomeric gp120 core in the b12- and CD4/17b-bound conformations into the density maps derived by electron tomography, we derive molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound states. We demonstrate that CD4 binding results in a major reorganization of the Env trimer, causing an outward rotation and displacement of each gp120 monomer. This appears to be coupled with a rearrangement of the gp41 region along the central axis of the trimer, leading to closer contact between the viral and target cell membranes. Our findings elucidate the structure and conformational changes of trimeric HIV-1 gp120 relevant to antibody neutralization and attachment to target cells.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Remark 0THIS ENTRY 3J70 CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5020) DETERMINED ...THIS ENTRY 3J70 CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5020) DETERMINED ORIGINALLY BY AUTHORS: J.LIU, A.BARTESAGHI, M.J.BORGNIA, G.SAPIRO, S.Y.SUBRAMANIAM

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-5020
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Structure viewerMolecule:
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Assembly

Deposited unit
A: monoclonal antibody 17b light chain
B: monoclonal antibody 17b heavy chain
C: T-cell surface glycoprotein CD4
D: Envelope glycoprotein gp120
E: envelope glycoprotein gp41
M: monoclonal antibody 17b light chain
N: monoclonal antibody 17b heavy chain
O: T-cell surface glycoprotein CD4
P: Envelope glycoprotein gp120
Q: envelope glycoprotein gp41
R: monoclonal antibody 17b light chain
S: monoclonal antibody 17b heavy chain
T: T-cell surface glycoprotein CD4
U: Envelope glycoprotein gp120
V: envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)391,38415
Polymers391,38415
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody monoclonal antibody 17b light chain


Mass: 22636.338 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody monoclonal antibody 17b heavy chain


Mass: 22816.270 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 20503.260 Da / Num. of mol.: 3 / Fragment: UNP residues 26-208 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01730
#4: Protein Envelope glycoprotein gp120 / Surface protein gp120 / SU / Glycoprotein 120 / gp120


Mass: 52572.652 Da / Num. of mol.: 3 / Fragment: UNP residues 31-500 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: P04578
#5: Protein envelope glycoprotein gp41 / Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 11932.701 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1
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: gp120, including variable regions, in complex with CD4 and 17b
Type: COMPLEX
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 34000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GENERIC CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 20 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms26016 0 0 0 26016

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