8H2N

gp96 RNA polymerase from P23-45 phage (crystal 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail.

Chaban, A.Minakhin, L.Goldobina, E.Bae, B.Hao, Y.Borukhov, S.Putzeys, L.Boon, M.Kabinger, F.Lavigne, R.Makarova, K.S.Koonin, E.V.Nair, S.K.Tagami, S.Severinov, K.Sokolova, M.L.

(2024) Nat Commun 15: 317-317

  • DOI: https://doi.org/10.1038/s41467-023-44630-z
  • Primary Citation of Related Structures:  
    8F5M, 8H2M, 8H2N

  • PubMed Abstract: 

    Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.


  • Organizational Affiliation

    Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tape tail measure protein
A, B, C, D
821Oshimavirus P2345Mutation(s): 0 
Gene Names: P23p96
UniProt
Find proteins for A7XXD0 (Thermus virus P23-45)
Explore A7XXD0 
Go to UniProtKB:  A7XXD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7XXD0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.158α = 90
b = 128.91β = 96.84
c = 136.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H01328, 22H01346

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Database references