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- EMDB-5936: Electron cryo-microscopy of the Moloney murine leukemia virus fur... -

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Basic information

Entry
Database: EMDB / ID: 5936
TitleElectron cryo-microscopy of the Moloney murine leukemia virus furin precursor Env in its native form
Map dataReconstruction of the native furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus
SampleNative form of furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus:
gp90
KeywordsFurin precursor / Moloney murine leukemia virus / Env maturation
SourceMoloney murine leukemia virus
Methodsingle particle reconstruction / cryo EM / 22 Å resolution
AuthorsSjoberg M / Wu SR / Loving R / Rantalainen K / Lindqvist B / Garoff H
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Furin cleavage of the Moloney murine leukemia virus Env precursor reorganizes the spike structure.
Authors: Mathilda Sjöberg / Shang-Rung Wu / Robin Löving / Kimmo Rantalainen / Birgitta Lindqvist / Henrik Garoff
DateDeposition: Mar 28, 2014 / Header (metadata) release: Apr 9, 2014 / Map release: Apr 9, 2014 / Last update: May 14, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5936.map.gz (map file in CCP4 format, 433 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
3.5 Å/pix.
= 168. Å
48 pix
3.5 Å/pix.
= 168. Å
48 pix
3.5 Å/pix.
= 168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density
Contour Level:2.1 (by author), 2.1 (movie #1):
Minimum - Maximum-2.57583761 - 6.81486845
Average (Standard dev.)0.02116431 (0.89234978)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions484848
Origin-7-7-7
Limit404040
Spacing484848
CellA=B=C: 168 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000168.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-7-7-7
NC/NR/NS484848
D min/max/mean-2.5766.8150.021

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Supplemental data

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Sample components

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Entire Native form of furin cleavage deficient mutant (R466G/K468G) Env ...

EntireName: Native form of furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus
Details: Affinity purified, gradient separated protein in 0.05% Triton X-100
Number of components: 1 / Oligomeric State: trimer
MassTheoretical: 270 kDa / Experimental: 500 kDa / Measured by: Estimated from Blue native PAGE

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Component #1: protein, gp90

ProteinName: gp90 / a.k.a: Furin precursor / Oligomeric Details: Trimer / Recombinant expression: No / Number of Copies: 3
MassTheoretical: 270 kDa / Experimental: 500 kDa
SourceSpecies: Moloney murine leukemia virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 50 mM HEPES, 100 mM NaCl, 1.8 mM CaCl2, pH 7.4
pH: 7.4
Support film400 mesh holey carbon grid, glow discharged
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 90 %
Method: Blotted for 3 seconds before plunging in liquid ethane, followed by transfer into liquid nitrogen.

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Electron microscopy imaging

ImagingMicroscope: JEOL 2100F / Date: Jan 25, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 9 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 43200 X (nominal), 43200 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected using online FFT.
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 95 K ( 93 - 96 K)
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1213 / Sampling size: 3.5 microns / Bit depth: 14

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 30 / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 9802
Details: The particles were selected using a semi-automatic selection program in EMAN.
3D reconstructionAlgorithm: back projection / Euler angles: EMAN / Software: EMAN1, EMAN2 / CTF correction: Each particle
Details: Final maps were calculated from seven averaged datasets. The particles were selected using an automatic selection program. Damaged particles were removed after visual inspection.
Resolution: 22 Å / Resolution method: FSC 0.5, semi-independent

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