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

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Basic information

Entry
Database: EMDB / ID: 2100
TitleLocation of the dsRNA-dependent polymerase, VP1, in rotavirus particles
Keywordsrotavirus / dsRNA-dependent / polymerase
SampleRotavirus DLP+VP1
SourceBovine rotavirus / virus / Rotavirus
Map datareconstruction of rotavirus DLP+VP1 (polymerase)
Methodsingle particle (icosahedral) reconstruction, at 6 A resolution
AuthorsEstrozi LF / Settembre EC / Goret G / McClain B / Zhang X / Chen JZ / Grigorieff N / Harrison SC
CitationJ. Mol. Biol., 2013, 425, 124-132

J. Mol. Biol., 2013, 425, 124-132 StrPapers
Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles.
Leandro F Estrozi / Ethan C Settembre / Gaël Goret / Brian McClain / Xing Zhang / James Z Chen / Nikolaus Grigorieff / Stephen C Harrison

DateDeposition: May 14, 2012 / Header (metadata) release: Jun 14, 2012 / Map release: Jun 14, 2012 / Last update: May 14, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0004844
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0004844
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4au6
  • Surface level: 0.0004844
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_2100.map.gz (map file in CCP4 format, 21362 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
1.7 A/pix
= 237.5 A
279 pix
1.7 A/pix
= 473.304 A
140 pix
1.7 A/pix
= 237.5 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.69643 A
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)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions279140140
Origin-1390-139
Limit1391390
Spacing279140140
CellA: 237.5 A / B: 473.30356 A / C: 237.5 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-0.0040.0080.000

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Supplemental data

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Sample components

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Entire Rotavirus DLP+VP1

EntireName: 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

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Component #1: protein, Rotavirus polymerase (VP1)

ProteinName: Rotavirus polymerase (VP1) / a.k.a: VP1
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 / Recombinant expression: No
MassTheoretical: 126.326 kDa
SourceSpecies: Bovine rotavirus / virus / Rotavirus

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Component #2: protein, VP1

ProteinName: VP1 / a.k.a: VP1 / Recombinant expression: No
SourceSpecies: Bovine rotavirus / virus / Rotavirus

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Component #3: protein, VP2

ProteinName: VP2 / a.k.a: VP2 / Recombinant expression: No
SourceSpecies: Bovine rotavirus / virus / Rotavirus

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Component #4: protein, VP3

ProteinName: VP3 / a.k.a: VP3 / Recombinant expression: No
SourceSpecies: Bovine rotavirus / virus / Rotavirus

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Component #5: nucleic-acid, dsRNA

Nucleic-acidName: dsRNA / a.k.a: dsRNA / Class: RNA / Structure: OTHER / Synthetic: No
SourceSpecies: Bovine rotavirus / virus / Rotavirus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.4
Support filmLacy carbon and C-flat
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 30 % / Method: Blot for 3 seconds before plunging
Details: Vitrification instrument: Home-made. Vitrification carried out in air at room temperature

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Jun 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 56540 X (calibrated) / Astigmatism: Objective lens astigmatism was corrected / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1100 - 3500 nm
Specimen HolderHolder: Eucentric, side-entry / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 386 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 1
URL of raw data: http://emlab.rose2.brandeis.edu/rotavirusdlp

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 7000 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Symmetry adapted functions based protocol / Software: RIco, and, FPM / CTF correction: Phase flipping for each particle / Resolution: 6 A / Resolution method: Comparison with X-ray map
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Software: URO and VEDA / Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: RECIPROCAL
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
Input PDB model: 2R7O
Chain ID: A
Output model

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