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Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation

by single particle (icosahedral) reconstruction, at 8.3 A resolution

Movie

Orientation:

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

#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5428
AuthorsMatsui T, Lander GC, Khayat R, Johnson JE
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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Diagram

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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 32, Page 14111-5, Year 2010
TitleSubunits fold at position-dependent rates during maturation of a eukaryotic RNA virus.
AuthorsTsutomu Matsui, Gabriel C Lander, Reza Khayat, John E Johnson
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
KeywordsCapsid, Cryoelectron Microscopy, Eukaryota (virology), Kinetics, Particle Size, RNA Viruses (physiology), Virus Assembly
LinksDOI: 10.1073/pnas.1004221107, PubMed: 20660783, PMC: PMC2922577
Map
FileEMD-5428.map ( map file in CCP4 format, 32002 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:1.0 (by author), 1 (movie #1):
Minimum - Maximum: -4.57011175 - 7.01301813
Average (Standard dev.): 0E-8 (0.99999994)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 200 200 200
Origin : -100 -100 -100
Limit : 99 99 99
Spacing : 200 200 200
Unit CellA = 553.6 A , B = 553.6 A , C = 553.6 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.768 A , Y = 2.768 A , Z = 2.768 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.7682.7682.768
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z553.600553.600553.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.5707.013-0.000
Annotation DetailsReconstruction of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Supplement
Sample
NameNudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
Number of Components1
Oligomeric StateIcosahedral virus
Component #1: virus - NwV (N omega V)
Scientific nameNudaurelia capensis omega virus
Common NameNwV (N omega V)
Scientific Name of SpeciesNudaurelia capensis omega virus (NCBI Taxonomy: 12541)
Common Name of SpeciesNwV (N omega V)
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRUS-LIKE PARTICLE
Natural SourceHost Species: Lepidoptera (NCBI Taxonomy: 7088)
Host Category: INVERTEBRATES
ShellDiameter: 400 A
T Number: 4
Experiment
Sample Preparation
Specimen Conc10 mg/ml
Specimen Stateparticle
BufferDetails: 100mM NaOAc, 250mM NaCl
pH: 5.0
Vitrification
MethodBlot for 5sec before plunging
Cryogen NameETHANE
Humidity100
InstrumentFEI VITROBOT MARK I
Temperature90 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Date13-FEB-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose16.5 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000 X,
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 3000 nm
Specimen Holder
Holder ( GATAN LIQUID NITROGEN )
Camera
Image Acquisition
Number of Digital Images295
DetailsData were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline.
Processing
Methodsingle particle (icosahedral) reconstruction
3 D reconstruction
AlgorithmProjection matching
SoftwareEMAN
CTF CorrectionEach image
DetailsData processing was performed using the Appion pipeline.
Resolution By Author8.3
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections23392
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5428.xml (7.1 KB)
Map dataemd_5428.map.gz (12.5 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5428
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.8 KB