8F5M | pdb_00008f5m

Crystal structure of P74 gp62

• PDB DOI: https://doi.org/10.2210/pdb8F5M/pdb

• Classification: REPLICATION
• Organism(s): Oshimavirus P7426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-14 Released: 2024-01-17 
• Deposition Author(s): Bae, B., Nair, S.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 137.32 kDa 
• Atom Count: 10,150 
• Modeled Residue Count: 1,183 
• Deposited Residue Count: 1,234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp62	A, B	617	Oshimavirus P7426	Mutation(s): 0  Gene Names: P74p62
UniProt
Find proteins for A7XXN5 (Thermus phage P74-26) Explore A7XXN5  Go to UniProtKB:  A7XXN5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.937	α = 90
b = 210.102	β = 90
c = 181.089	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Bae, B., Nair, S.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release