EMDB-2100: Location of the dsRNA-dependent polymerase, VP1, in ro...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 2100
Title	Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles
Map	reconstruction of rotavirus DLP+VP1 (polymerase)
Sample	Rotavirus DLP+VP1
Keywords	rotavirus, dsRNA-dependent, polymerase
Authors	Estrozi LF, Settembre EC, Goret G, McClain B, Zhang X, Chen JZ, Grigorieff N, Harrison SC
Date	Deposition: 2012-05-14, Header release: 2012-06-14, Map release: 2012-06-14, Last update: 2013-01-09
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.0004844, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.0004844, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-4au6, Surface level: 0.0004844, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-4au6, Made by Jmol
Supplemental images	emd_2100.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-4au6 CiteFit PDB-4f5x Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram PDB-1xi4 PDB-1xi5 PDB-2ymr List of similar structure data about Omokage system

Article
Citation - Primary
Article	J. Mol. Biol., Vol. 425, Issue 1, Page 124-32, Year 2013
Title	Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles.
Authors	Leandro 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.
Keywords	Capsid (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
Links	PII: S0022-2836(12)00829-7, DOI: 10.1016/j.jmb.2012.10.011, PubMed: 23089332, PMC: PMC3540981

Map

File

EMD-2100.map ( map file in CCP4 format, 21875 KB )

Projections & Slices

Size of images:

Axes	Z (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:	0.0004844 (by author), 0.0004844 (movie #1):
Minimum - Maximum:	-0.00405112 - 0.00763549
Average (Standard dev.):	4.119E-5 (0.00069179)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	279	140	140
Origin	-139	0	-139
Limit	139	139	0
Spacing	279	140	140

Unit Cell

A: 237.5 A, B: 473.30356 A, C: 237.5 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 1.69643 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	1.6964285714286	1.6964301075269	1.6964285714286
M x/y/z	140	279	140
origin x/y/z	0.000	0.000	0.000
length x/y/z	237.500	473.304	237.500
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	128	128	168
MAP C/R/S	1	2	3
start NC/NR/NS	0	-139	-139
NC/NR/NS	140	279	140
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-0.004	0.008	0.000

Annotation Details

reconstruction of rotavirus DLP+VP1 (polymerase)

Supplement
Images
Images	emd_2100.png
FSC
FSC

Sample
Name	Rotavirus DLP+VP1
Number of Components	5
Oligomeric State	780 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 name	Rotavirus polymerase (VP1)
Common Name	VP1
Theoretical Mass	0.126326 MDa
Details	The 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 Copies	11
Scientific Name of Species	Bovine rotavirus
Common Name of Species	Rotavirus
NCBI taxonomy	10927
Recombinant expression	No
Component #2: protein - VP1
Scientific name	VP1
Scientific Name of Species	Bovine rotavirus
Common Name of Species	Rotavirus
NCBI taxonomy	10927
Recombinant expression	No
Component #3: protein - VP2
Scientific name	VP2
Scientific Name of Species	Bovine rotavirus
Common Name of Species	Rotavirus
NCBI taxonomy	10927
Recombinant expression	No
Component #4: protein - VP3
Scientific name	VP3
Scientific Name of Species	Bovine rotavirus
Common Name of Species	Rotavirus
NCBI taxonomy	10927
Recombinant expression	No
Component #5: nucleic-acid - dsRNA
Scientific name	dsRNA
Scientific Name of Species	Bovine rotavirus
Common Name of Species	Rotavirus
NCBI taxonomy	10927
Synthetic	No
Class	RNA
Structure	OTHER

Experiment
Sample Preparation
Specimen Conc	5 mg/ml
Specimen Support Details	Lacy carbon and C-flat
Specimen State	particle
Buffer	pH: 7.4
Vitrification
Method	Blot for 3 seconds before plunging
Cryogen Name	ETHANE
Details	Vitrification instrument: Home-made. Vitrification carried out in air at room temperature
Humidity	30
Instrument	HOMEMADE PLUNGER
Imaging
Microscope	FEI TECNAI F30
Date	01-JUN-2007
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 59000, Calibrated: 56540
Astigmatism	Objective lens astigmatism was corrected
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1100 nm - 3500 nm
Specimen Holder
Holder	Eucentric, side-entry
Model	GATAN LIQUID NITROGEN
Temperature	90 K
Camera
Detector	Kodak SO163 film
Image Acquisition
Od Range	1
Scanner	ZEISS SCAI
Number of Digital Images	386
URL of Raw Data	http://emlab.rose2.brandeis.edu/rotavirusdlp
Sampling Size	7
Quant Bit Number	8

Processing
Method	single particle (icosahedral) reconstruction
3D reconstruction
Algorithm	Symmetry adapted functions based protocol
Software	RIco, and, FPM
CTF Correction	Phase flipping for each particle
Resolution By Author	6 A
Resolution Method	Comparison with X-ray map
Single Particle
Number of Projections	7000
Applied Symmetry	I (icosahedral)
Atomic Model Fitting
Model #0
Target Criteria	Correlation coefficient
Details	Protocol: 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
Software	URO and VEDA
Refinement Protocol	rigid body
Refinement Space	RECIPROCAL
PDB Entry ID	2R7O PDB-2r7o
PDB Chain ID	A
Fitted Coordinate
PDB entry ID	PDB-4au6

Download

Data from EMDB

Header (meta data in XML format)

emd-2100.xml (11.2 KB)

Map data

emd_2100.map.gz (7.8 MB)

Images

emd_2100.png (207 KB)

FSC (resolution estimation)

emd_2100_fsc.xml (130.3 KB)

FTP directory

ftp://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