[English] 日本語
Yorodumi
- EMDB-6407: In situ structures of the segmented genome and RNA polymerase com... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6407
TitleIn situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus
Map dataWhole map of quiescent CPV
SampleCPV capsid with VP4 + polymerase complex (TEC):
virus / RNA polymerase
Keywordscryo-EM / dsRNA genome organization / viral polymerase
SourceBombyx mori cypovirus 1 (Cytoplasmic polyhedrosis virus) / Bombyx mori (domestic silkworm)
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
DateDeposition: Aug 1, 2015 / Header (metadata) release: Aug 19, 2015 / Map release: Oct 28, 2015 / Last update: Dec 2, 2015

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -0.002
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: -0.002
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_6407.map.gz (map file in CCP4 format, 1339845 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
700 pix
1.01 Å/pix.
= 707. Å
700 pix
1.01 Å/pix.
= 707. Å
700 pix
1.01 Å/pix.
= 707. 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:0.006 (by emdb), -0.002 (movie #1):
Minimum - Maximum-0.02975343 - 0.03157998
Average (Standard dev.)-0.00855460 (0.00481324)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions700700700
Origin110110110
Limit809809809
Spacing700700700
CellA=B=C: 707.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z707.000707.000707.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-35-13026
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS110110110
NC/NR/NS700700700
D min/max/mean-0.0300.032-0.009

-
Supplemental data

-
Sample components

-
Entire CPV capsid with VP4 + polymerase complex (TEC)

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

-
Component #1: virus, Bombyx mori cypovirus 1

VirusName: Bombyx mori cypovirus 1 / a.k.a: Cytoplasmic polyhedrosis virus / Class: VIRION / Enveloped: No / Empty: No / Isolate: SPECIES
SpeciesSpecies: Bombyx mori cypovirus 1 (Cytoplasmic polyhedrosis virus)
Source (natural)Host Species: Bombyx mori (domestic silkworm) / Host category: INVERTEBRATES

-
Component #2: protein, RNA polymerase

ProteinName: RNA polymerase / Recombinant expression: No
SourceSpecies: Bombyx mori (domestic silkworm)

-
Experimental details

-
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

-
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)

-
Image acquisition

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

-
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

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more