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- EMDB-5418: Subunit organization of the membrane-bound HIV-1 envelope glycopr... -

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Basic information

Entry
Database: EMDB / ID: EMD-5418
TitleSubunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer
Map dataReconstruction of the membrane-bound HIV-1 envelope glycoprotein trimer precursor
Sample
  • Sample: The membrane-bound HIV-1 envelope glycoprotein trimer precursor
  • Protein or peptide: HIV-1 envelope glycoprotein trimer precursor
KeywordsHIV-1 / envelope glycoprotein / virus entry
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsMao Y / Wang L / Gu C / Herschhorn A / Xiang SH / Haim H / Yang X / Sodroski J
CitationJournal: Nat Struct Mol Biol / Year: 2012
Title: Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
Authors: Youdong Mao / Liping Wang / Christopher Gu / Alon Herschhorn / Shi-Hua Xiang / Hillel Haim / Xinzhen Yang / Joseph Sodroski /
Abstract: The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus- ...The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus-neutralizing antibodies. The mature Env spike results from cleavage of a trimeric glycoprotein precursor, gp160, into three gp120 and three gp41 subunits. Here, we describe an ~11-Å cryo-EM structure of the trimeric HIV-1 Env precursor in its unliganded state. The three gp120 and three gp41 subunits form a cage-like structure with an interior void surrounding the trimer axis. Interprotomer contacts are limited to the gp41 transmembrane region, the torus-like gp41 ectodomain and a trimer-association domain of gp120 composed of the V1, V2 and V3 variable regions. The cage-like architecture, which is unique among characterized viral envelope proteins, restricts antibody access, reflecting requirements imposed by HIV-1 persistence in the host.
History
DepositionMay 3, 2012-
Header (metadata) releaseJul 12, 2012-
Map releaseAug 15, 2012-
UpdateAug 15, 2012-
Current statusAug 15, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5418.jpg

Downloads & links

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Map

FileDownload / File: emd_5418.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the membrane-bound HIV-1 envelope glycoprotein trimer precursor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.99 Å/pix.
x 80 pix.
= 239.2 Å		2.99 Å/pix.
x 80 pix.
= 239.2 Å		2.99 Å/pix.
x 80 pix.
= 239.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.07084963 - 0.15849437
Average (Standard dev.)0.00000176 (±0.00686896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 239.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.992.992.99
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z239.200239.200239.200
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/NS808080
D min/max/mean-0.0710.1580.000

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Supplemental data

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Sample components

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Entire : The membrane-bound HIV-1 envelope glycoprotein trimer precursor

EntireName: The membrane-bound HIV-1 envelope glycoprotein trimer precursor
Components
  • Sample: The membrane-bound HIV-1 envelope glycoprotein trimer precursor
  • Protein or peptide: HIV-1 envelope glycoprotein trimer precursor

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Supramolecule #1000: The membrane-bound HIV-1 envelope glycoprotein trimer precursor

SupramoleculeName: The membrane-bound HIV-1 envelope glycoprotein trimer precursor
type: sample / ID: 1000
Details: The membrane glycoprotein was monodisperse and solubilized in detergents.
Oligomeric state: trimer / Number unique components: 1
Molecular weightExperimental: 440 KDa / Theoretical: 435 KDa / Method: Sedimentation, SDS-PAGE

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Macromolecule #1: HIV-1 envelope glycoprotein trimer precursor

MacromoleculeName: HIV-1 envelope glycoprotein trimer precursor / type: protein_or_peptide / ID: 1 / Name.synonym: Env trimer, gp160 trimer
Details: The membrane glycoprotein is solubilized in detergents.
Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: JF-FL / synonym: HIV-1 / Location in cell: Plasma membrane
Molecular weightExperimental: 440 KDa / Theoretical: 435 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pcDNA3.1 in 293F cell line

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris-HCl, 300 mM NaCl, 0.01% Cymal-6
GridDetails: 200 or 400 mesh copper grid with thin holey carbon support, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 89 K / Max: 93 K / Average: 91 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateAug 1, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 200835 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 150000
Sample stageSpecimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, XIMPP / Number images used: 90306

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