9DR1

E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state

• PDB DOI: https://doi.org/10.2210/pdb9DR1/pdb
• EM Map EMD-47120: EMDB EMDataResource

• Classification: TRANSFERASE/DNA/RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-24 Released: 2024-10-09 
• Deposition Author(s): Porta, J.C., Ellinger, E., Liu, Y., Walter, N.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis of RNA-mediated regulation of transcriptional pausing.

Porta, J.C., Ellinger, E., Liu, Y., Chauvier, A., Walter, N.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 384.86 kDa 
• Atom Count: 26,245 
• Modelled Residue Count: 3,242 
• Deposited Residue Count: 3,320 
• Unique protein chains: 4
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	C [auth G], D [auth H]	231	Escherichia coli	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	E [auth I]	1,340	Escherichia coli	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	F [auth J]	1,358	Escherichia coli	Mutation(s): 0  Gene Names: rpoC, EcE24377A_4529 EC: 2.7.7.6
UniProt
Find proteins for A7ZUK2 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZUK2  Go to UniProtKB:  A7ZUK2

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	G [auth K]	79	Escherichia coli	Mutation(s): 0  Gene Names: rpoZ, Ecok1_36260, APECO1_2812 EC: 2.7.7.6
UniProt
Find proteins for A1AHI0 (Escherichia coli O1:K1 / APEC) Explore A1AHI0  Go to UniProtKB:  A1AHI0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (39-MER)	A	30	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (30-MER)	B	30	Escherichia coli

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*GP*UP*AP*UP*CP*AP*CP*UP*AP*CP*UP*GP*GP*UP*AP*GP*GP*AP*GP*U)-3')	H [auth R]	21	Escherichia coli

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3
MODEL REFINEMENT	PHENIX	1.20_4459:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Porta, J.C., Ellinger, E., Liu, Y., Walter, N.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM131922

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release