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Electron cryo-microscopy of the Moloney murine leukemia virus furin precursor Env in its native form

by single particle reconstruction, at 22 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.1, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2.1, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5936
TitleElectron cryo-microscopy of the Moloney murine leukemia virus furin precursor Env in its native form
MapReconstruction 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
KeywordsFurin precursor, Moloney murine leukemia virus, Env maturation
AuthorsSjoberg M, Wu SR, Loving R, Rantalainen K, Lindqvist B, Garoff H
DateDeposition: 2014-03-28, Header release: 2014-04-09, Map release: 2014-04-09, Last update: 2014-05-14
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.1, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2.1, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 111, Issue 16, Page 6034-6039, Year 2014
TitleFurin cleavage of the Moloney murine leukemia virus Env precursor reorganizes the spike structure.
AuthorsMathilda Sjöberg, Shang-Rung Wu, Robin Löving, Kimmo Rantalainen, Birgitta Lindqvist, Henrik Garoff
Department of Biosciences and Nutrition, Karolinska Institute, S-141 57 Huddinge, Sweden.
KeywordsAnimals, Electrophoresis, Polyacrylamide Gel, Furin (metabolism, 3.4.21.75), Gene Products, env (chemistry), Humans, Immunoglobulin Fab Fragments (metabolism), Mice, Models, Molecular, Molecular Weight, Moloney murine leukemia virus (metabolism), Mutant Proteins (chemistry), Protein Multimerization, Trypsin (metabolism, 3.4.21.4)
LinksPubMed: 24711391, DOI: 10.1073/pnas.1317972111, PMC: PMC4000802
Map
Fileemd_5936.map.gz ( map file in CCP4 format, 433 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
3.5 A/pix
= 168. A
48 pix
3.5 A/pix
= 168. A
48 pix
3.5 A/pix
= 168. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.1 (by author), 2.1 (movie #1):
Minimum - Maximum: -2.57583761 - 6.81486845
Average (Standard dev.): 0.02116431 (0.89234978)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions484848
Origin-7-7-7
Limit404040
Spacing484848
Unit CellA= B= C: 168 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.5 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-7-7-7
NC/NR/NS484848
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.5766.8150.021
Annotation DetailsReconstruction of the native furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus
Supplement
Sample
NameNative form of furin cleavage deficient mutant (R466G/K468G) Env of Moloney murine leukemia virus
Number of Components1
Oligomeric Statetrimer
Theoretical Mass0.27MDa
DetailsAffinity purified, gradient separated protein in 0.05% Triton X-100
Mass-estimation MethodEstimated from Blue native PAGE
Experimental Mass0.5MDa
Component #1: protein - Furin precursor
Scientific namegp90
Common NameFurin precursor
Theoretical Mass0.27 MDa
Experimental Mass0.5 MDa
Oligomeric DetailsTrimer
Number of Copies3
Scientific Name of SpeciesMoloney murine leukemia virus
NCBI taxonomy11801
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.1 mg/ml
Specimen Support Details400 mesh holey carbon grid, glow discharged
BufferDetails: 50 mM HEPES, 100 mM NaCl, 1.8 mM CaCl2, pH 7.4
pH: 7.4
Vitrification
MethodBlotted for 3 seconds before plunging in liquid ethane, followed by transfer into liquid nitrogen.
Cryogen NameETHANE
Humidity90
InstrumentFEI VITROBOT MARK II
Temperature77 Kelvin
Imaging
MicroscopeJEOL 2100F
Date25-JAN-2013
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose9 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 43200, Calibrated: 43200
AstigmatismObjective lens astigmatism was corrected using online FFT.
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2500 nm - 4000 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Temperature95 K ( 93 - 96 K)
Camera
DetectorTVIPS TEMCAM-F416 (4k x 4k)
Image Acquisition
#1
Number of Digital Images1213
Sampling Size3.5
Quant Bit Number14
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmback projection
Euler Angles DetailsEMAN
SoftwareEMAN1, EMAN2
CTF CorrectionEach particle
DetailsFinal maps were calculated from seven averaged datasets. The particles were selected using an automatic selection program. Damaged particles were removed after visual inspection.
Resolution By Author22 A
Resolution MethodFSC 0.5, semi-independent
Single Particle
Number of Class Averages30
Applied SymmetryC3 (3 fold cyclic)
Number of Projections9802
DetailsThe particles were selected using a semi-automatic selection program in EMAN.
Download
Data from EMDB
Header (meta data in XML format)emd-5936.xml (8 KB)
Map dataemd_5936.map.gz (343.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5936
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.7 KB