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- EMDB-5020: Molecular Structure of the Native HIV-1 gp120 trimer bound to CD4... -

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Basic information

Entry
Database: EMDB / ID: EMD-5020
TitleMolecular Structure of the Native HIV-1 gp120 trimer bound to CD4 and 17b: Spike region
Map dataCD4 and 17b-bound HIV-1 BaL spike
Sample
  • Sample: HIV-1 BaL virus
  • Virus: envelope glycoprotein (unknown)
KeywordsHIV-1 / envelope glycoprotein. immunodeficiency virus / gp120
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 / Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / MHC class II protein binding ...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 / Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / MHC class II protein binding / positive regulation of kinase activity / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of establishment of T cell polarity / 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 / Dectin-2 family / 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 plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / actin filament organization / host cell endosome membrane / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / Assembly Of The HIV Virion / calcium-mediated signaling / Budding and maturation of HIV virion / positive regulation of protein phosphorylation / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / signaling receptor activity / Clathrin-mediated endocytosis / virus receptor activity / response to ethanol / defense response to Gram-negative bacterium / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of viral entry into host cell / early endosome / 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 / viral protein processing / immune response / membrane raft / receptor ligand activity / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / endoplasmic reticulum membrane / protein kinase binding / 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 / 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 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesenvelope glycoprotein (unknown)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsBartesaghi A / Borgnia M / Liu J / Sapiro G / Subramaniam S
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
DepositionJun 29, 2008-
Header (metadata) releaseJul 3, 2008-
Map releaseMay 5, 2009-
UpdateAug 2, 2011-
Current statusAug 2, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3dno
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j70
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5020_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5020.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCD4 and 17b-bound HIV-1 BaL spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.431 / Movie #1: 1.5
Minimum - Maximum-0.466446 - 8.846080000000001
Average (Standard dev.)0.0424989 (±0.388842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 410 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.4668.8460.042

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Supplemental data

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Sample components

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Entire : HIV-1 BaL virus

EntireName: HIV-1 BaL virus
Components
  • Sample: HIV-1 BaL virus
  • Virus: envelope glycoprotein (unknown)

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Supramolecule #1000: HIV-1 BaL virus

SupramoleculeName: HIV-1 BaL virus / type: sample / ID: 1000
Details: Structures determined by cryo-electron tomography combined with 3D averaging
Number unique components: 1

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Supramolecule #1: envelope glycoprotein

SupramoleculeName: envelope glycoprotein / type: virus / ID: 1 / Name.synonym: envelope glycoprotein / Sci species name: envelope glycoprotein / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: envelope glycoprotein
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 7.2 / Details: 0.01 M Tris, 0.1 M NaCl, 1 mM EDTA
GridDetails: home-made holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot and plunge

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 77 K
Specialist opticsEnergy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 80 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 34000
Sample stageSpecimen holder: Cartridge / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsAverage number of tilts used in the 3D reconstructions: 400. Average tomographic tilt angle increment: 1.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD and in-house procedures

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Atomic model buiding 1

Initial modelPDB ID:

1gc1

SoftwareName: Chimera
DetailsAutomated fitting procedures
RefinementSpace: REAL / Target criteria: correlation coefficient
Output model

PDB-3dno:
Molecular structure for the HIV-1 gp120 trimer in the CD4-bound state

PDB-3j70:
Model of gp120, including variable regions, in complex with CD4 and 17b

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