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- EMDB-5233: CryoEM structure of cytoplasmic polyhedrosis virus -

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Basic information

Entry
Database: EMDB / ID: 5233
TitleCryoEM structure of cytoplasmic polyhedrosis virus
Keywordscryoelectron microscopy
SampleCytoplasmic Polyhedrosis Virus
SourceCypovirus / virus / CPV
Map dataThis is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus
Methodsingle particle (icosahedral) reconstruction, at 3.9 Å resolution
AuthorsCheng L / Sun J / Zhang K / Mou Z / Huang X / Ji G / Sun F / Zhang J / Zhu P
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 1373-1378

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 1373-1378 Yorodumi Papers
Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.
Lingpeng Cheng / Jingchen Sun / Kai Zhang / Zongjun Mou / Xiaoxing Huang / Gang Ji / Fei Sun / Jingqiang Zhang / Ping Zhu

Validation ReportPDB-ID: 3iz3

SummaryFull reportAbout validation report
DateDeposition: Sep 14, 2010 / Header (metadata) release: Mar 10, 2011 / Map release: Mar 10, 2011 / Last update: Apr 2, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3iz3
  • Imaged by Jmol
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Supplemental images

Downloads & links

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Map

Fileemd_5233.map.gz (map file in CCP4 format, 800001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
500 pix
1.19 Å/pix.
= 595. Å
640 pix
1.19 Å/pix.
= 761.6 Å
640 pix
1.19 Å/pix.
= 761.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.19 Å
Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-16.95112991 - 18.03697586
Average (Standard dev.)0E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions640640500
Origin-320-3200
Limit319319499
Spacing640640500
CellA: 761.60004 Å / B: 761.60004 Å / C: 595 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.191.191.19
M x/y/z640640500
origin x/y/z0.0000.0000.000
length x/y/z761.600761.600595.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-320-3200
NC/NR/NS640640500
D min/max/mean-16.95118.0370.000

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Supplemental data

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Sample components

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Entire Cytoplasmic Polyhedrosis Virus

EntireName: Cytoplasmic Polyhedrosis Virus / Number of components: 5

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Component #1: virus, Cypovirus

VirusName: Cypovirus / a.k.a: CPV / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Cypovirus / virus / CPV
Source (natural)Host Species: Bombyx mori / arthropod / カイコ, カイコガ /
Host category: INVERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
Support film200 mesh
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 10, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: OTHER
LensMagnification: 75000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2800 nm
Specimen HolderModel: OTHER
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1600 / Sampling size: 1.19 microns / Bit depth: 24

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 29000 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: cross-common lines / Software: IMIRS / CTF correction: Each micrograph / Resolution: 3.9 Å / Resolution method: FSC 0.143

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Atomic model buiding

Output model

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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

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