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- EMDB-2863: Surface rendered vitrified native Env -

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Basic information

Entry
Database: EMDB / ID: EMD-2863
TitleSurface rendered vitrified native Env
Map dataSurface rendered vitrified native Env
Sample
  • Sample: Native Env
  • Protein or peptide: Moloney murine leukemia virus
KeywordsCryo-electron microscopy / Env trimers / image processing / isomerization arrested state / receptor binding domain
Biological speciesMoloney murine leukemia virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å
AuthorsWu S-R / Sjoberg M / Wallin M / Lindqvist B / Ekstrom M / Hebert H / Koeck P / Garoff H
CitationJournal: EMBO J / Year: 2008
Title: Turning of the receptor-binding domains opens up the murine leukaemia virus Env for membrane fusion.
Authors: Shang-Rung Wu / Mathilda Sjöberg / Michael Wallin / Birgitta Lindqvist / Maria Ekström / Hans Hebert / Philip J B Koeck / Henrik Garoff /
Abstract: The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We ...The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We have arrested Env activation at a stage prior to isomerization by alkylating the active thiol in SU and compared the structure of isomerization-arrested Env with that of native Env. Env trimers of respective form were isolated from solubilized particles by sedimentation and their structures were reconstructed from electron microscopic images of both vitrified and negatively stained samples. We found that the protomeric unit of both trimers formed three protrusions, a top, middle and a lower one. The atomic structure of the receptor-binding domain of SU fitted into the upper protrusion. This was formed similar to a bent finger. Significantly, in native Env the tips of the fingers were directed against each other enclosing a cavity below, whereas they had turned outward in isomerization-arrested Env transforming the cavity into an open well. This might subsequently guide the fusion peptides in extended TM subunits into the target membrane.
History
DepositionAug 22, 2008-
Header (metadata) releaseAug 26, 2008-
Map releaseAug 27, 2009-
UpdateJul 8, 2015-
Current statusJul 8, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-2863.gif

Downloads & links

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Map

FileDownload / File: emd_2863.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendered vitrified native Env
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.77 Å/pix.
x 48 pix.
= 180.881 Å		3.77 Å/pix.
x 48 pix.
= 180.881 Å		3.77 Å/pix.
x 48 pix.
= 180.881 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.76835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-5.40174 - 5.47187
Average (Standard dev.)-0.000277643 (±0.82736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-24-24-24
Dimensions484848
Spacing484848
CellA=B=C: 180.881 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.76835416666673.76835416666673.7683541666667
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z180.881180.881180.881
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-5.4025.472-0.000

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Supplemental data

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Supplemental map: emd 2863 additional 1.map

Fileemd_2863_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native Env

EntireName: Native Env
Components
  • Sample: Native Env
  • Protein or peptide: Moloney murine leukemia virus

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Supramolecule #1000: Native Env

SupramoleculeName: Native Env / type: sample / ID: 1000 / Oligomeric state: Trimer / Number unique components: 1
Molecular weightExperimental: 200 KDa / Method: Gel electrophoresis

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Macromolecule #1: Moloney murine leukemia virus

MacromoleculeName: Moloney murine leukemia virus / type: protein_or_peptide / ID: 1 / Name.synonym: Mo-MLV Env
Details: Moloney murine leukemia virus ICTvDb ID 00.061.1.02.014.00.001.
Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: No
Source (natural)Organism: Moloney murine leukemia virus / Tissue: Virus / Cell: MOV-3, NIH 3T3
Molecular weightExperimental: 200 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 20 mM HEPES, 135 mM NaCl, pH 7.45, 1.8 mM CaCl2, 0.15 % Triton X-100, 12 % (w/w) sucrose
StainingType: NEGATIVE / Details: No staining
GridDetails: 400 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3 seconds twice before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 93 K / Max: 96 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected using online FFT
DateMay 10, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 30 µm / Number real images: 80 / Average electron dose: 9 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 86000
Sample stageSpecimen holder: Eucentric / 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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 7057
Final two d classificationNumber classes: 131

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