[English] 日本語
Yorodumi
- EMDB-8982: Icosahedral cryo-EM structure of immature Kunjin virus -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8982
TitleIcosahedral cryo-EM structure of immature Kunjin virus
Map dataIcosahedral reconstruction of immature Kunjin virus.
SampleKunjin virus (STRAIN MRM61C):
virus / Glycoprotein shell / Nucleocapsid core
SourceKunjin virus (STRAIN MRM61C)
Methodsingle particle reconstruction / cryo EM / 10 Å resolution
AuthorsTherkelsen MD / Klose T / Vago F / Jiang W / Rossmann MG / Kuhn RJ
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Flaviviruses have imperfect icosahedral symmetry.
Authors: Matthew D Therkelsen / Thomas Klose / Frank Vago / Wen Jiang / Michael G Rossmann / Richard J Kuhn
DateDeposition: Jul 21, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_8982.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
3.24 Å/pix.
= 1036.8 Å
320 pix
3.24 Å/pix.
= 1036.8 Å
320 pix
3.24 Å/pix.
= 1036.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.24 Å
Density
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.01619139 - 0.054041628
Average (Standard dev.)0.00003626431 (0.004936031)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin6.06.06.0
Limit325.0325.0325.0
Spacing320320320
CellA=B=C: 1036.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.243.243.24
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1036.8001036.8001036.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS666
NC/NR/NS320320320
D min/max/mean-0.0160.0540.000

-
Supplemental data

-
Sample components

-
Entire Kunjin virus (STRAIN MRM61C)

EntireName: Kunjin virus (STRAIN MRM61C)
Details: Immature Kunjin virus purified from ammonium chloride-treated C6/36 cells.
Number of components: 3

-
Component #1: virus, Kunjin virus (STRAIN MRM61C)

VirusName: Kunjin virus (STRAIN MRM61C) / Class: VIRION
Details: Immature Kunjin virus purified from ammonium chloride-treated C6/36 cells.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Kunjin virus (STRAIN MRM61C)
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: capsid shell / Diameter: 560.0 Å / T number(triangulation number): 3

-
Component #2: cellular-component, Glycoprotein shell

Cellular-componentName: Glycoprotein shell / Recombinant expression: No
SourceSpecies: Kunjin virus (STRAIN MRM61C)

-
Component #3: cellular-component, Nucleocapsid core

Cellular-componentName: Nucleocapsid core / Recombinant expression: No
SourceSpecies: Kunjin virus (STRAIN MRM61C)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 % / Details: Blot for 6 seconds before plunging..

-
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: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.0 - 80.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 387

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 7396
3D reconstructionSoftware: RELION / Resolution: 1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

+
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