8H2M | pdb_00008h2m

gp96 RNA polymerase from P23-45 phage (crystal 1)

• PDB DOI: https://doi.org/10.2210/pdb8H2M/pdb

• Classification: TRANSCRIPTION
• Organism(s): Oshimavirus P2345
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-06 Released: 2023-10-11 
• Deposition Author(s): Chaban, A., Sokolova, M.L., Tagami, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 
  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

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

• PubMed: 38182597 
• DOI: https://doi.org/10.1038/s41467-023-44630-z
• Primary Citation 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.

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Organizational Affiliation: 
• Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany.
Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, 19107, USA.
APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, 08084-1489, USA.
Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium.
Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. [e-mail].
RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. [e-mail].
Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. [e-mail].
Institute of Molecular Genetics National Kurchatov Center, Moscow, 123182, Russia. [e-mail].
Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia. [e-mail].
Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 134.99 kDa 
• Atom Count: 5,938 
• Modeled Residue Count: 754 
• Deposited Residue Count: 1,214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tape tail measure protein	A	1,214	Oshimavirus P2345	Mutation(s): 0  Gene Names: P23p96
UniProt
Find proteins for A7XXD0 (Thermus virus P23-45) Explore A7XXD0  Go to UniProtKB:  A7XXD0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.78	α = 90
b = 137.78	β = 90
c = 135.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Chaban, A., Sokolova, M.L., Tagami, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H01328, 22H01346

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Structure summary