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- EMDB-6408: In situ structures of the segmented genome and RNA polymerase com... -

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Basic information

Entry
Database: EMDB / ID: 6408
TitleIn situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus
Map dataAveraged qCPV TEC
SampleCPV VP4 + polymerase complex (TEC):
VP4 / RNA polymerase
Keywordscryo-EM / dsRNA genome organization / viral polymerase
Function / homologyRNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / viral genome replication / RNA-directed 5'-3' RNA polymerase activity / GTP binding / RNA binding / RNA-dependent RNA polymerase / VP1 / Viral structural protein 4
Function and homology information
SourceBombyx mori cypovirus 1 (Cytoplasmic polyhedrosis virus)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsZhang X / Ding K / Yu XK / Chang W / Sun JC / Zhou ZH
CitationJournal: Nature / Year: 2015
Title: In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus.
Authors: Xing Zhang / Ke Ding / Xuekui Yu / Winston Chang / Jingchen Sun / Z Hong Zhou
Validation ReportPDB-ID: 3jb6

SummaryFull reportAbout validation report
DateDeposition: Aug 1, 2015 / Header (metadata) release: Aug 19, 2015 / Map release: Oct 28, 2015 / Last update: Dec 2, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3jb6
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6408.map.gz (map file in CCP4 format, 11918 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
142 pix
1.01 Å/pix.
= 143.42 Å
131 pix
1.01 Å/pix.
= 132.31 Å
164 pix
1.01 Å/pix.
= 165.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density
Contour Level:1.5 (by emdb), 2 (movie #1):
Minimum - Maximum-8.85126591 - 15.05303574
Average (Standard dev.)0E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions131164142
Origin46-111107
Limit17652248
Spacing164131142
CellA: 132.31 Å / B: 165.64 Å / C: 143.42 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z131164142
origin x/y/z0.0000.0000.000
length x/y/z132.310165.640143.420
α/β/γ90.00090.00090.000
start NX/NY/NZ46-111107
NX/NY/NZ131164142
MAP C/R/S213
start NC/NR/NS-11146107
NC/NR/NS164131142
D min/max/mean-8.85115.053-0.000

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Supplemental data

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Sample components

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Entire CPV VP4 + polymerase complex (TEC)

EntireName: CPV VP4 + polymerase complex (TEC) / Number of components: 2

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Component #1: protein, VP4

ProteinName: VP4 / Recombinant expression: No
SourceSpecies: Bombyx mori cypovirus 1 (Cytoplasmic polyhedrosis virus)

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Component #2: protein, RNA polymerase

ProteinName: RNA polymerase / Recombinant expression: No
SourceSpecies: Bombyx mori cypovirus 1 (Cytoplasmic polyhedrosis virus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 70 mM Tris-Cl, 10 mM MgCl2, 100 mM NaCl, 2 mM GTP
pH: 8
Support film200 mesh Quantifoil holey carbon film
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Jul 26, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 49000 X (nominal), 49500 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 4500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80 K
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4385 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 1 / Applied symmetry: C1 (asymmetric) / Number of projections: 68526
3D reconstructionSoftware: Frealign / CTF correction: Each particle / Resolution: 3.3 Å / Resolution method: FSC 0.143, semi-independent

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Atomic model buiding

Output model

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