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CryoEM structure of cytoplasmic polyhedrosis virus

by single particle (icosahedral) reconstruction, at 3.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3, Image by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-3iz3, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5233
TitleCryoEM structure of cytoplasmic polyhedrosis virus
MapThis is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus
SampleCytoplasmic Polyhedrosis Virus
Keywordscryoelectron microscopy
AuthorsCheng L, Sun J, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J, Zhu P
DateDeposition: 2010-09-14, Header release: 2011-03-10, Map release: 2011-03-10, Last update: 2012-04-02
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3, Image by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-3iz3, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3iz3

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 4, Page 1373-8, Year 2011
TitleAtomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.
AuthorsLingpeng Cheng, Jingchen Sun, Kai Zhang, Zongjun Mou, Xiaoxing Huang, Gang Ji, Fei Sun, Jingqiang Zhang, Ping Zhu
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.
KeywordsAmino Acid Sequence, Capsid (metabolism), Capsid Proteins (chemistry), Cryoelectron Microscopy (methods), Models, Molecular, Models, Structural, Molecular Sequence Data, Molecular Structure, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, RNA Caps, RNA, Messenger (genetics), RNA, Viral (genetics), Reoviridae (genetics), Sequence Homology, Amino Acid
LinksDOI: 10.1073/pnas.1014995108, PubMed: 21220303, PMC: PMC3029759
Map
Fileemd_5233.map.gz ( map file in CCP4 format, 800001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
500 pix
1.19 A/pix
= 595. A
640 pix
1.19 A/pix
= 761.6 A
640 pix
1.19 A/pix
= 761.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum: -16.95112991 - 18.03697586
Average (Standard dev.): 0E-8 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions640640500
Origin-320-3200
Limit319319499
Spacing640640500
Unit CellA: 761.60004 A, B: 761.60004 A, C: 595 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.19 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.191.191.19
M x/y/z640640500
origin x/y/z0.0000.0000.000
length x/y/z761.600761.600595.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-320-3200
NC/NR/NS640640500
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-16.95118.0370.000
Annotation DetailsThis is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus
Supplement
Images
Images
Sample
NameCytoplasmic Polyhedrosis Virus
Number of Components5
Component #1: virus - CPV
Scientific nameCypovirus
Common NameCPV
Scientific Name of SpeciesCypovirus
Common Name of SpeciesCPV
NCBI taxonomy10981
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 7091
Host Species: Bombyx mori
Host Category: INVERTEBRATES
ShellID: 1 , Diameter: 720 A, T Number: 1
Experiment
Sample Preparation
Specimen Support Details200 mesh
Specimen Stateparticle
BufferpH: 7.5
Vitrification
MethodBlot for 4 seconds before plunging
Cryogen NameETHANE
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeFEI TITAN KRIOS
Date10-APR-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose20 e/A**2
Illumination ModeOTHER
Lens
MagnificationCalibrated: 75000
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 2800 nm
Specimen Holder
ModelOTHER
Camera
DetectorGENERIC GATAN (4k x 4k)
Image Acquisition
#1
Number of Digital Images1600
Sampling Size1.19
Quant Bit Number24
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmcross-common lines
SoftwareIMIRS
CTF CorrectionEach micrograph
Resolution By Author3.9 A
Resolution MethodFSC 0.143
Single Particle
Number of Projections29000
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5233.xml (6.8 KB)
Map dataemd_5233.map.gz (672.2 MB)
Imagesemd_5233_1.jpg (165.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5233
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.1 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.4 MB