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- EMDB-20596: BmCPV virion with SAM -

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Basic information

Entry
Database: EMDB / ID: EMD-20596
TitleBmCPV virion with SAM
Map dataBmCPV virion with SAM
SampleBombyx mori cypovirus 1 != Bombyx mori cytoplasmic polyhedrosis virus

Bombyx mori cypovirus 1

  • Virus: Bombyx mori cytoplasmic polyhedrosis virus
Biological speciesBombyx mori cytoplasmic polyhedrosis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCui YX / Zhang YN / Sun JC / Zhou ZH
Funding support China, United States, 8 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31672489 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Conservative transcription in three steps visualized in a double-stranded RNA virus.
Authors: Yanxiang Cui / Yinong Zhang / Kang Zhou / Jingchen Sun / Z Hong Zhou /
Abstract: Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV) ...Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV). Because of the lack of in situ structures of the intermediate stages of RNA-dependent RNA polymerase (RdRp) during transcription, it is poorly understood how RdRp detects environmental cues and internal transcriptional states to initiate and coordinate repeated cycles of transcript production inside the capsid. Here, we captured five high-resolution (2.8-3.5 Å) RdRp-RNA in situ structures-representing quiescent, initiation, early elongation, elongation and abortive states-under seven experimental conditions of CPV. We observed the 'Y'-form initial RNA fork in the initiation state and the complete transcription bubble in the elongation state. These structures reveal that de novo RNA transcription involves three major conformational changes during state transitions. Our results support an ouroboros model for endogenous conservative transcription in dsRNA viruses.
History
DepositionAug 13, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseNov 20, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20596.png

Downloads & links

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Map

FileDownload / File: emd_20596.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBmCPV virion with SAM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 800 pix.
= 849.6 Å		1.06 Å/pix.
x 800 pix.
= 849.6 Å		1.06 Å/pix.
x 800 pix.
= 849.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06689491 - 0.13166766
Average (Standard dev.)0.0027930955 (±0.010084142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 849.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z849.600849.600849.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.0670.1320.003

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Supplemental data

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Sample components

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Entire : Bombyx mori cypovirus 1

EntireName: Bombyx mori cypovirus 1
Components
  • Virus: Bombyx mori cytoplasmic polyhedrosis virus

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Supramolecule #1: Bombyx mori cytoplasmic polyhedrosis virus

SupramoleculeName: Bombyx mori cytoplasmic polyhedrosis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 110829
Sci species name: Bombyx mori cytoplasmic polyhedrosis virus
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bombyx mori (domestic silkworm)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22465
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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