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- EMDB-5272: Molecular Structure of Unliganded Native SIVmneE11S gp120 trimer:... -

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Basic information

Entry
Database: EMDB / ID: EMD-5272
TitleMolecular Structure of Unliganded Native SIVmneE11S gp120 trimer: Spike region
Map data3D Average of Envelope Glycoproteins from SIVmneE11S - structures determined by cryo-electron tomography combined with 3D averaging
Sample
  • Sample: SIVmneE11S virus
  • Protein or peptide: envelope glycoprotein from Simian Immunodeficiency virus (clone E11S) infecting Macaca nemestrina
KeywordsAntigens / CD4 / cryo-electron microscopy / HIV / SIV / envelope glycoprotein / gp120 / gp41 / HIV-1 / Immunoglobulin Fab Fragments
Biological speciesunidentified (others)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsWhite TA / Bartesaghi A / Borgnia M / Subramaniam S
CitationJournal: PLoS Pathog / Year: 2010
Title: Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.
Authors: Tommi A White / Alberto Bartesaghi / Mario J Borgnia / Joel R Meyerson / M Jason V de la Cruz / Julian W Bess / Rachna Nandwani / James A Hoxie / Jeffrey D Lifson / Jacqueline L S Milne / Sriram Subramaniam /
Abstract: The initial step in target cell infection by human, and the closely related simian immunodeficiency viruses (HIV and SIV, respectively) occurs with the binding of trimeric envelope glycoproteins (Env) ...The initial step in target cell infection by human, and the closely related simian immunodeficiency viruses (HIV and SIV, respectively) occurs with the binding of trimeric envelope glycoproteins (Env), composed of heterodimers of the viral transmembrane glycoprotein (gp41) and surface glycoprotein (gp120) to target T-cells. Knowledge of the molecular structure of trimeric Env on intact viruses is important both for understanding the molecular mechanisms underlying virus-cell interactions and for the design of effective immunogen-based vaccines to combat HIV/AIDS. Previous analyses of intact HIV-1 BaL virions have already resulted in structures of trimeric Env in unliganded and CD4-liganded states at ~20 Å resolution. Here, we show that the molecular architectures of trimeric Env from SIVmneE11S, SIVmac239 and HIV-1 R3A strains are closely comparable to that previously determined for HIV-1 BaL, with the V1 and V2 variable loops located at the apex of the spike, close to the contact zone between virus and cell. The location of the V1/V2 loops in trimeric Env was definitively confirmed by structural analysis of HIV-1 R3A virions engineered to express Env with deletion of these loops. Strikingly, in SIV CP-MAC, a CD4-independent strain, trimeric Env is in a constitutively "open" conformation with gp120 trimers splayed out in a conformation similar to that seen for HIV-1 BaL Env when it is complexed with sCD4 and the CD4i antibody 17b. Our findings suggest a structural explanation for the molecular mechanism of CD4-independent viral entry and further establish that cryo-electron tomography can be used to discover distinct, functionally relevant quaternary structures of Env displayed on intact viruses.
History
DepositionApr 12, 2011-
Header (metadata) releaseJun 6, 2011-
Map releaseJun 6, 2011-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5272_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5272.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D Average of Envelope Glycoproteins from SIVmneE11S - structures determined by cryo-electron tomography combined with 3D averaging
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.8
Minimum - Maximum-3.90685 - 8.37289
Average (Standard dev.)0.0258687 (±0.598025)
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-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-3.9078.3730.026

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Supplemental data

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Sample components

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Entire : SIVmneE11S virus

EntireName: SIVmneE11S virus
Components
  • Sample: SIVmneE11S virus
  • Protein or peptide: envelope glycoprotein from Simian Immunodeficiency virus (clone E11S) infecting Macaca nemestrina

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Supramolecule #1000: SIVmneE11S virus

SupramoleculeName: SIVmneE11S virus / type: sample / ID: 1000
Details: Structures determined by cryo-electron tomography combined with 3D averaging
Oligomeric state: trimer / Number unique components: 1

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Macromolecule #1: envelope glycoprotein from Simian Immunodeficiency virus (clone E...

MacromoleculeName: envelope glycoprotein from Simian Immunodeficiency virus (clone E11S) infecting Macaca nemestrina
type: protein_or_peptide / ID: 1 / Name.synonym: Env
Details: Envelope glycoproteins present on the surface of intact virions. Virus infecting Macaca nemestrina (Pig-tailed macaque)
Oligomeric state: trimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others) / Strain: SIVmneE11S / synonym: Simian Immunodeficiency Virus / Cell: HUT-78 / Location in cell: viral membrane
Molecular weightTheoretical: 480 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 7.5 / Details: TNE Buffer (10 mM Tris, 150 mM NaCl, 1 mM EDTA)
GridDetails: 200 mesh Quantifoil Multi A
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III
Details: Vitrification instrument: Mark III Vitrobot (FEI, Netherlands)
Method: blot for 6 seconds, at 25 C, 100 percent humidity, blot offset of -2, into an ethane slurry cooled by liquid nitrogen

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 34000
Specialist opticsEnergy filter - Name: GATAN GIF / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Cartridge / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °
TemperatureMin: 81 K / Max: 82 K / Average: 81 K
DetailsAreas were selected for proper ice thickness (about 200 nm).
DateMay 14, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 150 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD
Details: Please see A. Bartesaghi, et al. Journal of Structural Biology, 2008
DetailsAverage tomographic tilt angle increment: 1.

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Atomic model buiding 1

Initial modelPDB ID:

3dnn

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid body. Automated fitting procedures
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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