[English] 日本語
Yorodumi
- EMDB-3286: Evidence for a conformational switch in Influenzavirus M1 and its... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3286
TitleEvidence for a conformational switch in Influenzavirus M1 and its role in filamentous virion architecture
Map dataReconstruction of inner membrane leaflet, M1 and attached densities at leading virion tips
SampleLeading tip of filamentous Influenza A virions including inner leaflet, M1 and internal crown:
virus
KeywordsInfluenza A virus / FLUAV / polymerase / M1 / crown / leading tip / trailing tip / filamentous
SourceInfluenza A virus (Influenza virus)
Methodsubtomogram averaging / cryo EM / 76 Å resolution
AuthorsKiss G / Abdulsattar BO / Phapugrangkul P / Birch K / Jones IM / Neuman BW
CitationJournal: To Be Published
Title: Evidence for a conformational switch in Influenzavirus M1 and its role in filamentous virion architecture
Authors: Kiss G / Abdulsattar BO / Phapugrangkul P / Birch K / Jones IM / Neuman BW
DateDeposition: Dec 17, 2015 / Header (metadata) release: Oct 12, 2016 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.52
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3286.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
10 Å/pix.
= 640. Å
64 pix
10 Å/pix.
= 640. Å
64 pix
10 Å/pix.
= 640. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10 Å
Density
Contour Level:0.52 (by author), 0.52 (movie #1):
Minimum - Maximum-3.09326649 - 3.06961107
Average (Standard dev.)4.166E-5 (0.28897005)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
CellA=B=C: 640 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z101010
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z640.000640.000640.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-3.0933.0700.000

-
Supplemental data

-
Sample components

-
Entire Leading tip of filamentous Influenza A virions including inner le...

EntireName: Leading tip of filamentous Influenza A virions including inner leaflet, M1 and internal crown
Details: Compare to matched image of the opposite virion tip
Number of components: 1

-
Component #1: virus, Influenza A virus

VirusName: Influenza A virus / a.k.a: Influenza virus / Class: VIRION
Details: Reconstruction of the inner layer of the viral envelope and attached densities likely representing polymerase molecules from native virions of mixed A/Aichi/X31 and A/Udorn strains. Map is Gaussian filtered to 7.6 nm the 0.5 FSC. Reconstructed in EMAN2.
Empty: No / Enveloped: Yes / Isolate: OTHER
SpeciesSpecies: Influenza A virus (Influenza virus)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: MDCK
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Host species strain: Combined A/Aichi/2/68 and A/Udorn/307/72
Shell #1Name of element: M1

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Method: Blotted 4s before plunging
Details: Details for EM and reconstruction published in Calder et al., Proc Natl Acad Sci U S A. 2010 Jun 8; 107(23): 10685 to 10690.

-
Electron microscopy imaging

ImagingMicroscope: OTHER / Date: Jan 1, 2010
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI EAGLE (2k x 2k)

-
Image acquisition

Image acquisitionURL of raw data: https://cryoem.nimr.mrc.ac.uk/recent-projects/

-
Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 23 / Applied symmetry: C1 (asymmetric) / Number of class averages: 2
Details: Subtomograms were manually selected. Alignments and cropping of the region of interest was done interactively with EMAN2.
3D reconstructionSoftware: MRC, IMOD, IVE / Resolution: 76 Å / Resolution method: FSC 0.5, gold-standard
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