5FJ7

Structure of the P2 polymerase inside in vitro assembled bacteriophage phi6 polymerase complex, with P1 included


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Localized Reconstruction of Subunits from Electron Cryomicroscopy Images of Macromolecular Complexes.

Ilca, S.L.Kotecha, A.Sun, X.Poranen, M.M.Stuart, D.I.Huiskonen, J.T.

(2015) Nat Commun 6: 8843

  • DOI: 10.1038/ncomms9843
  • Primary Citation of Related Structures:  
    5FJ6, 5FJ5, 5FJ7

  • PubMed Abstract: 
  • Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution ...

    Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems.


    Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR INNER PROTEIN P1A, B761Pseudomonas virus phi6Mutation(s): 0 
Gene Names: P1
UniProt
Find proteins for P11126 (Pseudomonas phage phi6)
Explore P11126 
Go to UniProtKB:  P11126
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASEC664Pseudomonas virus phi6Mutation(s): 0 
Gene Names: P2
EC: 2.7.7.48
UniProt
Find proteins for P11124 (Pseudomonas phage phi6)
Explore P11124 
Go to UniProtKB:  P11124
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth C]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-11-20
    Changes: Derived calculations