5NWT | pdb_00005nwt

Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex

• PDB DOI: https://doi.org/10.2210/pdb5NWT/pdb
• Entry: 5NWT supersedes: 5BYH

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12, Klebsiella pneumoniae subsp. rhinoscleromatis SB3432
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-08 Released: 2017-09-13 
• Deposition Author(s): Zhang, X., Buck, M., Darbari, V.C., Yang, Y., Zhang, N., Lu, D., Glyde, R., Wang, Y., Winkelman, J., Gourse, R.L., Murakami, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.76 Å
• R-Value Free: 
  0.370 (Depositor), 0.372 (DCC) 
• R-Value Work: 
  0.313 (Depositor), 0.316 (DCC) 
• R-Value Observed: 
  0.316 (Depositor) 

Starting Model: experimental

Literature

TRANSCRIPTION. Structures of the RNA polymerase-Sigma54 reveal new and conserved regulatory strategies.

Yang, Y., Darbari, V.C., Zhang, N., Lu, D., Glyde, R., Wang, Y.P., Winkelman, J.T., Gourse, R.L., Murakami, K.S., Buck, M., Zhang, X.

(2015) Science 349: 882-885

• PubMed: 26293966 
• DOI: https://doi.org/10.1126/science.aab1478
• Primary Citation Related Structures: 
  5EZK, 5NWT


• PubMed Abstract: 
  

  Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activators for initiation. Our crystal structure of the 450-kilodalton RNAP-σ(54) holoenzyme at 3.8 angstroms reveals molecular details of σ(54) and its interactions with RNAP. The structure explains how σ(54) targets different regions in RNAP to exert its inhibitory function. Although σ(54) and the major σ factor, σ(70), have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.

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Organizational Affiliation: 
• Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, China.
Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK.
Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, UK.
Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK.
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, China.
Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 440.88 kDa 
• Atom Count: 22,461 
• Modeled Residue Count: 3,707 
• Deposited Residue Count: 3,975 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	329	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4  Go to UniProtKB:  P0A7Z4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,342	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2  Go to UniProtKB:  P0A8V2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,407	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoC, tabB, b3988, JW3951 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7  Go to UniProtKB:  P0A8T7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	91	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800  Go to UniProtKB:  P0A800

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor	F [auth M]	477	Klebsiella pneumoniae subsp. rhinoscleromatis SB3432	Mutation(s): 0  Gene Names: rpoN, KPR_4804

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth D], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	F [auth M]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
UNK	F [auth M]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.76 Å
• R-Value Free:  0.370 (Depositor), 0.372 (DCC) 
• R-Value Work:  0.313 (Depositor), 0.316 (DCC) 
• R-Value Observed: 0.316 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.477	α = 90
b = 151.525	β = 90
c = 195.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Zhang, X., Buck, M., Darbari, V.C., Yang, Y., Zhang, N., Lu, D., Glyde, R., Wang, Y., Winkelman, J., Gourse, R.L., Murakami, K.S.
• This entry supersedes: 5BYH

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary