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Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles

by single particle (icosahedral) reconstruction, at 6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0004844, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0004844, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4au6, Surface level: 0.0004844, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-4au6, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2100
TitleLocation of the dsRNA-dependent polymerase, VP1, in rotavirus particles
Mapreconstruction of rotavirus DLP+VP1 (polymerase)
SampleRotavirus DLP+VP1
Keywordsrotavirus, dsRNA-dependent, polymerase
AuthorsEstrozi LF, Settembre EC, Goret G, McClain B, Zhang X, Chen JZ, Grigorieff N, Harrison SC
DateDeposition: 2012-05-14, Header release: 2012-06-14, Map release: 2012-06-14, Last update: 2013-01-09
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0004844, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0004844, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4au6, Surface level: 0.0004844, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-4au6, Image by Jmol

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

PDB-4au6

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Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 425, Issue 1, Page 124-32, Year 2013
TitleLocation of the dsRNA-dependent polymerase, VP1, in rotavirus particles.
AuthorsLeandro F Estrozi, Ethan C Settembre, Gaël Goret, Brian McClain, Xing Zhang, James Z Chen, Nikolaus Grigorieff, Stephen C Harrison
European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, Grenoble 38042, France.
KeywordsCapsid (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, Image Processing, Computer-Assisted, Models, Molecular, RNA, Double-Stranded (genetics), RNA, Messenger (genetics), RNA, Viral (genetics), Rotavirus (chemistry), VP1 protein, Rotavirus, Viral Core Proteins (chemistry), Virus Assembly
LinksPII: S0022-2836(12)00829-7, DOI: 10.1016/j.jmb.2012.10.011, PubMed: 23089332, PMC: PMC3540981
Map
Fileemd_2100.map.gz ( map file in CCP4 format, 21362 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
1.6964285714286 A/pix
= 237.5 A
279 pix
1.6964301075269 A/pix
= 473.304 A
140 pix
1.6964285714286 A/pix
= 237.5 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0004844 (by author), 0.0004844 (movie #1):
Minimum - Maximum: -0.00405112 - 0.00763549
Average (Standard dev.): 4.119E-5 (0.00069179)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions279140140
Origin-1390-139
Limit1391390
Spacing279140140
Unit CellA: 237.5 A, B: 473.30356 A, C: 237.5 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.69643 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.69642857142861.69643010752691.6964285714286
M x/y/z140279140
origin x/y/z0.0000.0000.000
length x/y/z237.500473.304237.500
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS0-139-139
NC/NR/NS140279140
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0040.0080.000
Annotation Detailsreconstruction of rotavirus DLP+VP1 (polymerase)
Supplement
Images
Images
FSC
FSC
Sample
NameRotavirus DLP+VP1
Number of Components5
Oligomeric State780 molecules of VP6 form a DLP particle with 12 molecules of VP1, 120 molecules of VP2, 12 molecules of VP3 and 11 dsRNA molecules
Component #1: protein - VP1
Scientific nameRotavirus polymerase (VP1)
Common NameVP1
Theoretical Mass0.126326 MDa
DetailsThe icosahedral 3D reconstruction of rotavirus DLP shows extra-density near the 5-fold axis corresponding to one copy of VP1 attached to the DLP inner surface.
Number of Copies11
Scientific Name of SpeciesBovine rotavirus
Common Name of SpeciesRotavirus
NCBI taxonomy10927
Recombinant expressionNo
Component #2: protein - VP1
Scientific nameVP1
Scientific Name of SpeciesBovine rotavirus
Common Name of SpeciesRotavirus
NCBI taxonomy10927
Recombinant expressionNo
Component #3: protein - VP2
Scientific nameVP2
Scientific Name of SpeciesBovine rotavirus
Common Name of SpeciesRotavirus
NCBI taxonomy10927
Recombinant expressionNo
Component #4: protein - VP3
Scientific nameVP3
Scientific Name of SpeciesBovine rotavirus
Common Name of SpeciesRotavirus
NCBI taxonomy10927
Recombinant expressionNo
Component #5: nucleic-acid - dsRNA
Scientific namedsRNA
Scientific Name of SpeciesBovine rotavirus
Common Name of SpeciesRotavirus
NCBI taxonomy10927
SyntheticNo
ClassRNA
StructureOTHER
Experiment
Sample Preparation
Specimen Conc5 mg/ml
Specimen Support DetailsLacy carbon and C-flat
Specimen Stateparticle
BufferpH: 7.4
Vitrification
MethodBlot for 3 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Home-made. Vitrification carried out in air at room temperature
Humidity30
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI TECNAI F30
Date01-JUN-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 59000, Calibrated: 56540
AstigmatismObjective lens astigmatism was corrected
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1100 nm - 3500 nm
Specimen Holder
HolderEucentric, side-entry
ModelGATAN LIQUID NITROGEN
Temperature90 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Od Range1
ScannerZEISS SCAI
Number of Digital Images386
URL of Raw Datahttp://emlab.rose2.brandeis.edu/rotavirusdlp
Sampling Size7
Quant Bit Number8
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmSymmetry adapted functions based protocol
SoftwareRIco, and, FPM
CTF CorrectionPhase flipping for each particle
Resolution By Author
6 A
Resolution MethodComparison with X-ray map
Single Particle
Number of Projections7000
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
Target CriteriaCorrelation coefficient
DetailsProtocol: Rigid body. The Fourier coefficients of VP1 were downweighted by a factor 5 in order to prevent VP1 from being "attracted" by the stronger density of the VP2/6 layer during the fit. matrix 1 0.286272 -0.958148 -0.000156 150.76188 0.573968 0.171358 0.800748 -71.02608 -0.767209 -0.229322 0.599001 -168.57402 matrix 2 -0.084128 -0.546853 -0.832991 184.93534 0.025364 -0.836859 0.546831 15.73129 -0.996132 0.024876 0.084274 -147.45338 matrix 3 0.245240 0.395934 -0.884926 125.30383 -0.558295 -0.688567 -0.462799 80.75011 -0.792568 0.607546 0.052184 -184.30794 matrix 4 0.819204 0.567290 -0.084182 54.27816 -0.370407 0.411304 -0.832843 34.17286 -0.437839 0.713450 0.547070 -228.20418 matrix 5 0.844563 -0.269594 0.462637 70.01368 0.329383 0.942768 -0.051920 -59.62970 -0.422162 0.196234 0.885026 -218.47982
SoftwareURO and VEDA
Refinement Protocolrigid body
Refinement SpaceRECIPROCAL
PDB Entry ID2R7O
PDB Chain IDA
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-2100.xml (11.2 KB)
Map dataemd_2100.map.gz (7.8 MB)
Imagesemd_2100.png (207 KB)
FSC (resolution estimation)emd_2100_fsc.xml (130.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2100
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5 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), 4.9 MB
Session file for UCSF-Chimera, 26.6 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 8.7 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB