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CryoEM reconstruction of the Marburg virus nucleocapsid.

by helical reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.00124, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.00124, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1986
TitleCryoEM reconstruction of the Marburg virus nucleocapsid.
MapThis is a map of the Marburg virus nucleocapsid within virions.
SampleMarburg virus nucleocapsid
KeywordsMarburg, virus, nucleocapsid, Nucleoprotein, VP24, VP35
AuthorsBharat TAM, Riches JD, Kolesnikova L, Welsch S, Kraehling V, Davey N, Parsy ML, Becker S, Briggs JAG
DateDeposition: 2011-11-11, Header release: 2011-11-17, Map release: 2011-11-17, Last update: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.00124, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.00124, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticlePLoS Biol., Vol. 9, Issue 11, Page e1001196, Year 2011
TitleCryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells.
AuthorsTanmay A M Bharat, James D Riches, Larissa Kolesnikova, Sonja Welsch, Verena Krähling, Norman Davey, Marie-Laure Parsy, Stephan Becker, John A G Briggs
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
KeywordsCell Line, Cryoelectron Microscopy, Electron Microscope Tomography, HEK293 Cells, Humans, Marburgvirus (chemistry), Nucleocapsid (metabolism), Nucleoproteins (metabolism), RNA, Viral, Rabies virus (physiology), VP24 protein, Marburg virus, VP35 protein, filovirus, Viral Proteins (chemistry), Viral Regulatory and Accessory Proteins (chemistry), Virus Assembly, Virus Release
LinksDOI: 10.1371/journal.pbio.1001196, PubMed: 22110401, PMC: PMC3217011
Map
Fileemd_1986.map.gz ( map file in CCP4 format, 7912 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
4 A/pix
= 360. A
150 pix
4 A/pix
= 600. A
150 pix
4 A/pix
= 600. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.00124 (by author), 0.00124 (movie #1):
Minimum - Maximum: -0.00187585 - 0.00387182
Average (Standard dev.): 0.00040353 (0.000906448)
Data TypeImage stored as Reals
Map Geometry
Axis orderXYZ
Dimensions15015090
Origin000
Limit14914989
Spacing15015090
Unit CellA: 600 A, B: 600 A, C: 360 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z444
M x/y/z15015090
origin x/y/z-0.000-0.000-0.000
length x/y/z600.000600.000360.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS15015090
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0020.0040.000
Annotation DetailsThis is a map of the Marburg virus nucleocapsid within virions.
Supplement
Images
Images
Sample
NameMarburg virus nucleocapsid
Number of Components1
Component #1: virus - Marburg virus
Scientific nameMarburg marburgvirus
Common NameMarburg virus
Scientific Name of SpeciesMarburg marburgvirus
Common Name of SpeciesMarburg virus
NCBI taxonomy11269
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
Experiment
Sample Preparation
Helical ParametersDelta Z: 5 A
Delta Phi: 24.3 degrees
Hand: LEFT HANDED
Specimen Statefilament
BufferDetails: PBS buffer with 4% PFA.
Vitrification
MethodPlunge freezing
Cryogen NameETHANE
DetailsVitrification instrument: Plunge freezer
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI/PHILIPS CM120T
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 37000
Nominal Cs6.3 mm
Imaging ModeBRIGHT FIELD
Defocus0.6 nm - 4 nm
Specimen Holder
HolderGatan 626
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerZEISS SCAI
Sampling Size14
Processing
Methodhelical reconstruction
3D reconstruction
Algorithmreal-space helical
SoftwareSpider, Bsoft
CTF CorrectionPhase flip
Resolution By Author25 A
Resolution MethodFSC 0.5
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body. 4 monomers from the VSV Nucleoprotein structure were fitted in as a single rigid body without any corrections.
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID2WYY
Download
Data from EMDB
Header (meta data in XML format)emd-1986.xml (7.1 KB)
Map dataemd_1986.map.gz (7.3 MB)
Imagesemd-1986.jpg (37.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1986
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 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), 3.1 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.7 KB