7S00 | pdb_00007s00

X-ray structure of the phage AR9 non-virion RNA polymerase core

• PDB DOI: https://doi.org/10.2210/pdb7S00/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus phage AR9
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-28 Released: 2022-07-06 
• Deposition Author(s): Leiman, P.G., Sokolova, M.L., Fraser, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.

Fraser, A., Sokolova, M.L., Drobysheva, A.V., Gordeeva, J.V., Borukhov, S., Jumper, J., Severinov, K.V., Leiman, P.G.

(2022) Nat Commun 13: 3526-3526

• PubMed: 35725571 
• DOI: https://doi.org/10.1038/s41467-022-31214-6
• Primary Citation Related Structures: 
  7S00, 7S01, 7UM0, 7UM1


• PubMed Abstract: 
  

  Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-0647, USA.
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-0647, USA. [e-mail].
Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia. [e-mail].
Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, 08084-1489, USA.
DeepMind Technologies Limited, London, UK.
Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia. [e-mail].
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia. [e-mail].
Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. [e-mail].
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-0647, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 520.41 kDa 
• Atom Count: 33,894 
• Modeled Residue Count: 4,145 
• Deposited Residue Count: 4,480 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase beta subunit	A [auth c], E [auth e]	496	Bacillus phage AR9	Mutation(s): 0  Gene Names: AR9_g105
UniProt
Find proteins for A0A172JI16 (Bacillus phage AR9) Explore A0A172JI16  Go to UniProtKB:  A0A172JI16

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase	B [auth C], F [auth E]	665	Bacillus phage AR9	Mutation(s): 0  Gene Names: AR9_g089 EC: 2.7.7.6
UniProt
Find proteins for A0A172JHZ2 (Bacillus phage AR9) Explore A0A172JHZ2  Go to UniProtKB:  A0A172JHZ2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase	C [auth D], G [auth F]	631	Bacillus phage AR9	Mutation(s): 0  Gene Names: AR9_g154 EC: 2.7.7.6
UniProt
Find proteins for A0A172JI62 (Bacillus phage AR9) Explore A0A172JI62  Go to UniProtKB:  A0A172JI62

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase beta' subunit	D [auth d], H [auth f]	448	Bacillus phage AR9	Mutation(s): 0  Gene Names: AR9_g270 EC: 2.7.7.6
UniProt
Find proteins for A0A172JIH0 (Bacillus phage AR9) Explore A0A172JIH0  Go to UniProtKB:  A0A172JIH0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	I [auth D], J [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.858	α = 90
b = 166.27	β = 90
c = 307.215	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Leiman, P.G., Sokolova, M.L., Fraser, A.

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Funding Organization	Location	Grant Number
Not funded		Funded by UTMB

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description