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- PDB-3jcc: Structure of Simian Immunodeficiency Virus Envelope Spikes bound ... -

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Basic information

Entry
Database: PDB / ID: 3jcc
TitleStructure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5
Components
  • Antibody 36D5 heavy chain
  • Antibody 36D5 light chain
  • Envelope glycoprotein gp120
  • T-cell surface glycoprotein CD4
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Cryoelectron tomography / immunology / AIDS / HIV / 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 / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / 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 / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / enzyme-linked receptor protein signaling pathway / Other interleukin signaling / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / T cell activation / positive regulation of interleukin-2 production / calcium-mediated signaling / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / virus receptor activity / signaling receptor activity / Clathrin-mediated endocytosis / MHC class II protein complex binding / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / cell adhesion / immune response / membrane raft / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / external side of plasma membrane / viral envelope / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / 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 / Gp120 core superfamily ...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 / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
Envelope glycoprotein gp120 / T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesSimian immunodeficiency virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM
AuthorsHu, G. / Liu, J. / Roux, K. / Taylor, K.A.
CitationJournal: J Virol / Year: 2017
Title: Structure of Simian Immunodeficiency Virus Envelope Spikes Bound with CD4 and Monoclonal Antibody 36D5.
Authors: Guiqing Hu / Jun Liu / Kenneth H Roux / Kenneth A Taylor /
Abstract: The human immunodeficiency virus type 1 (HIV-1)/simian immunodeficiency virus (SIV) envelope spike (Env) mediates viral entry into host cells. The V3 loop of the gp120 component of the Env trimer ...The human immunodeficiency virus type 1 (HIV-1)/simian immunodeficiency virus (SIV) envelope spike (Env) mediates viral entry into host cells. The V3 loop of the gp120 component of the Env trimer contributes to the coreceptor binding site and is a target for neutralizing antibodies. We used cryo-electron tomography to visualize the binding of CD4 and the V3 loop monoclonal antibody (MAb) 36D5 to gp120 of the SIV Env trimer. Our results show that 36D5 binds gp120 at the base of the V3 loop and suggest that the antibody exerts its neutralization effect by blocking the coreceptor binding site. The antibody does this without altering the dynamics of the spike motion between closed and open states when CD4 is bound. The interaction between 36D5 and SIV gp120 is similar to the interaction between some broadly neutralizing anti-V3 loop antibodies and HIV-1 gp120. Two conformations of gp120 bound with CD4 are revealed, suggesting an intrinsic dynamic nature of the liganded Env trimer. CD4 binding substantially increases the binding of 36D5 to gp120 in the intact Env trimer, consistent with CD4-induced changes in the conformation of gp120 and the antibody binding site. Binding by MAb 36D5 does not substantially alter the proportions of the two CD4-bound conformations. The position of MAb 36D5 at the V3 base changes little between conformations, indicating that the V3 base serves as a pivot point during the transition between these two states. Glycoprotein spikes on the surfaces of SIV and HIV are the sole targets available to the immune system for antibody neutralization. Spikes evade the immune system by a combination of a thick layer of polysaccharide on the surface (the glycan shield) and movement between spike domains that masks the epitope conformation. Using SIV virions whose spikes were "decorated" with the primary cellular receptor (CD4) and an antibody (36D5) at part of the coreceptor binding site, we visualized multiple conformations trapped by the rapid freezing step, which were separated using statistical analysis. Our results show that the CD4-induced conformational dynamics of the spike enhances binding of the antibody.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Database references / Category: citation / em_image_scans
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 30, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Assembly

Deposited unit
A: Envelope glycoprotein gp120
B: Antibody 36D5 light chain
C: Antibody 36D5 heavy chain
D: T-cell surface glycoprotein CD4
E: Envelope glycoprotein gp120
I: Envelope glycoprotein gp120


Theoretical massNumber of molelcules
Total (without water)217,2416
Polymers217,2416
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8460 Å2
ΔGint-46 kcal/mol
Surface area97120 Å2

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Components

#1: Protein Envelope glycoprotein gp120 /


Mass: 50130.594 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Simian immunodeficiency virus / Strain: SIV239/251tail/Supt-CCR5 CL.30 / References: UniProt: A0A3B6UDT5*PLUS
#2: Antibody Antibody 36D5 light chain


Mass: 22291.643 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody Antibody 36D5 heavy chain


Mass: 25115.289 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 19442.045 Da / Num. of mol.: 1 / Fragment: UNP residues 26-200 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01730
Sequence detailsENVELOPE GLYCOPROTEIN WAS FROM SIMIAN IMMUNODEFICIENCY VIRUS, BUT THE MODELED SEQUENCE IS FROM HIV-1.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: electron tomography

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Sample preparation

Component
IDNameTypeParent-ID
2Simian immunodeficiency virusVIRUS1
1SIV envelope spike bound to CD4 and monoclonal antibody 36d5 in the open stateCOMPLEX0
3T-cell surface glycoprotein CD4PROTEIN1
4monoclonal antibody 36D5PROTEIN1
Details of virusEmpty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Plunged into liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Aug 16, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 4000 nm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: unidentified / Tilt angle max: 65 ° / Tilt angle min: -65 °
Image recordingElectron dose: 100 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionNum. of particles: 1796 / Nominal pixel size: 5.7 Å / Actual pixel size: 5.7 Å / Details: (Subtomogram Averaging--Applied Symmetry: C1) / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4NCO
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms13909 0 0 0 13909

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