6R3B

BACTERIOPHAGE SPP1 PROCAPSID-I PROTEIN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural transitions during the scaffolding-driven assembly of a viral capsid.

Ignatiou, A.Brasiles, S.El Sadek Fadel, M.Burger, J.Mielke, T.Topf, M.Tavares, P.Orlova, E.V.

(2019) Nat Commun 10: 4840-4840

  • DOI: https://doi.org/10.1038/s41467-019-12790-6
  • Primary Citation of Related Structures:  
    6R3A, 6R3B, 6RTL

  • PubMed Abstract: 

    Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid protein (MCP) to build an icosahedral lattice. Here we report near-atomic resolution cryo-EM structures of the bacteriophage SPP1 procapsid, the intermediate expanded procapsid with partially released SPs, and the mature capsid with DNA. In the intermediate state, SPs are bound only to MCP pentons and to adjacent subunits from hexons. SP departure results in the expanded state associated with unfolding of the MCP N-terminus and straightening of E-loops. The newly formed extensive inter-capsomere bonding appears to compensate for release of SPs that clasp MCP capsomeres together. Subsequent DNA packaging instigates bending of MCP A domain loops outwards, closing the hexons central opening and creating the capsid auxiliary protein binding interface. These findings provide a molecular basis for the sequential structural rearrangements during viral capsid maturation.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London, WC1E 7HX, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A, B, C, D, E
A, B, C, D, E, F, G
323Bacillus phage SPP1Mutation(s): 0 
UniProt
Find proteins for Q38582 (Bacillus phage SPP1)
Explore Q38582 
Go to UniProtKB:  Q38582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38582
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC5
MODEL REFINEMENTCoot

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Other
  • Version 1.2: 2020-11-04
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Refinement description