3J9S

Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Measuring the optimal exposure for single particle cryo-EM using a 2.6 angstrom reconstruction of rotavirus VP6.

Grant, T.Grigorieff, N.

(2015) Elife 4: e06980-e06980

  • DOI: 10.7554/eLife.06980

  • PubMed Abstract: 
  • Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using ...

    Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 Å resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/Å(2), we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions, our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This 'high-exposure' technique should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.


    Organizational Affiliation

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Intermediate capsid protein VP6
A
398Rotavirus A (strain RVA/Cow/United Kingdom/UK/1975/G6P7[5])Mutation(s): 0 
Find proteins for P18610 (Rotavirus A (strain RVA/Cow/United Kingdom/UK/1975/G6P7[5]))
Go to UniProtKB:  P18610
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Database references
  • Version 1.2: 2015-07-01
    Type: Derived calculations
  • Version 1.3: 2015-09-02
    Type: Database references
  • Version 1.4: 2018-07-18
    Type: Data collection