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- EMDB-1813: Structural Comparison of HIV-1 Envelope Spikes with and without t... -

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Basic information

Entry
Database: EMDB / ID: EMD-1813
TitleStructural Comparison of HIV-1 Envelope Spikes with and without the V1V2 Loop.
Map dataThis is the map of the envelope glycoprotein of HIV-1.
Sample
  • Sample: Envelope glycoprotein
  • Protein or peptide: Envelope glycoprotein gp160
KeywordsVirus envelope.
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsHu G / Liu J / Taylor KA / Roux KH
CitationJournal: J Virol / Year: 2011
Title: Structural comparison of HIV-1 envelope spikes with and without the V1/V2 loop.
Authors: Guiqing Hu / Jun Liu / Kenneth A Taylor / Kenneth H Roux /
Abstract: We have used cryoelectron tomography of vitreous-ice-embedded HIV-1 virions to compare the envelope (Env) spikes of a wild-type strain with those of a mutant strain in which the V1/V2 loop has been ...We have used cryoelectron tomography of vitreous-ice-embedded HIV-1 virions to compare the envelope (Env) spikes of a wild-type strain with those of a mutant strain in which the V1/V2 loop has been deleted. Deletion of V1/V2 results in a spike with far more structural heterogeneity than is observed in the wild type, likely reflecting greatly enhanced gp120 protomer flexibility. A major difference between the two forms is a pronounced loss of mass from the "peak" of the native Env spike. The apparent loss of contact among three gp120 protomers likely accounts for the more open structure, heterogeneity in configuration, and previous observations that broadly neutralizing epitopes and reactive sites on other structural elements are more exposed in such constructs.
History
DepositionOct 25, 2010-
Header (metadata) releaseNov 5, 2010-
Map releaseFeb 17, 2012-
UpdateMar 14, 2012-
Current statusMar 14, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1813.png

Downloads & links

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Map

FileDownload / File: emd_1813.map.gz / Format: CCP4 / Size: 230.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of the envelope glycoprotein of HIV-1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.6 Å/pix.
x 49 pix.
= 225.4 Å		4.6 Å/pix.
x 35 pix.
= 161. Å		4.6 Å/pix.
x 35 pix.
= 161. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-1.72491527 - 1.55729318
Average (Standard dev.)-0.02505944 (±0.3956832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions353549
Spacing353549
CellA: 161.0 Å / B: 161.0 Å / C: 225.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.64.64.6
M x/y/z353549
origin x/y/z0.0000.0000.000
length x/y/z161.000161.000225.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS353549
D min/max/mean-1.7251.557-0.025

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Supplemental data

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Sample components

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Entire : Envelope glycoprotein

EntireName: Envelope glycoprotein
Components
  • Sample: Envelope glycoprotein
  • Protein or peptide: Envelope glycoprotein gp160

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Supramolecule #1000: Envelope glycoprotein

SupramoleculeName: Envelope glycoprotein / type: sample / ID: 1000 / Details: The sample was ice-embedded. / Number unique components: 1

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Name.synonym: Envelope glycoprotein / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Human immunodeficiency virus 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

GridDetails: Holey carbon grid
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Multi-specimen holer / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Protomo and I3

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Atomic model buiding 1

Initial modelPDB ID:

3jwd


Chain - Chain ID: A
SoftwareName: Manual
DetailsPDBEntryID_givenInChain. Protocol: Manual. The fitting was conducted manually in chimera. The V3 loop is built from the V3 loop of PDB 2B4C.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

3fus


Chain - Chain ID: A
SoftwareName: Manual
DetailsPDBEntryID_givenInChain. Protocol: Manual. The fitting was conducted manually in chimera. The V3 loop is built from the V3 loop of PDB 2B4C.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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