[English] 日本語
Yorodumi
- EMDB-8249: Subtomogram-averaged map of a single rubella virus capsid unit -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8249
TitleSubtomogram-averaged map of a single rubella virus capsid unit
Map dataSubtomogram-averaged single capsid unit
SampleRubella virus strain M33:
capsid proteinCapsid / ligand
Function / homologyRubella membrane glycoprotein E2 / Rubella capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1 / T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell ...Rubella membrane glycoprotein E2 / Rubella capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1 / T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral nucleocapsid / viral envelope / virion attachment to host cell / virion membrane / RNA binding / integral component of membrane / Structural polyprotein
Function and homology information
SourceRubella virus strain M33
Methodsubtomogram averaging / cryo EM / 35 Å resolution
AuthorsMangala Prasad V / Klose T
CitationJournal: PLoS Pathog. / Year: 2017
Title: Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Authors: Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann
Validation ReportPDB-ID: 5khe

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: May 10, 2017 / Last update: Sep 13, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.95
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.95
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5khe
  • Surface level: 1.95
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_8249.map.gz (map file in CCP4 format, 56 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
24 pix
5.28 Å/pix.
= 126.72 Å
24 pix
5.28 Å/pix.
= 126.72 Å
24 pix
5.28 Å/pix.
= 126.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.28 Å
Density
Contour Level:1.95 (by author), 1.95 (movie #1):
Minimum - Maximum-3.2933166 - 4.881808
Average (Standard dev.)0.2174404 (0.88683295)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions242424
Origin-12-12-12
Limit111111
Spacing242424
CellA=B=C: 126.72 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.285.285.28
M x/y/z242424
origin x/y/z0.0000.0000.000
length x/y/z126.720126.720126.720
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-12-12-12
NC/NR/NS242424
D min/max/mean-3.2934.8820.217

-
Supplemental data

-
Sample components

-
Entire Rubella virus strain M33

EntireName: Rubella virus strain M33 / Number of components: 3
MassTheoretical: 64 kDa

-
Component #1: protein, Rubella virus strain M33

ProteinName: Rubella virus strain M33 / Recombinant expression: No
MassTheoretical: 64 kDa
SourceSpecies: Rubella virus strain M33
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Vector: pTXB1 / Strain: BL21(DE3)

-
Component #2: protein, capsid protein

ProteinName: capsid proteinCapsid / Recombinant expression: No
MassTheoretical: 30.016332 kDa
Source (engineered)Expression System: Rubella virus

-
Component #3: ligand, water

LigandName: water / Number of Copies: 35 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.2
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 11000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 500 - nm
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: PEET / Resolution: 35 Å / Resolution method: OTHER

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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