7C97

Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA

• PDB DOI: https://doi.org/10.2210/pdb7C97/pdb
• NAKB: 7C97
• EM Map EMD-30307: EMDB EMDataResource

• Classification: TRANSFERASE/DNA
• Organism(s): Escherichia coli, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-05 Released: 2020-08-12 
• Deposition Author(s): Lin, W., Feng, Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7DY6

Literature

Structural basis for transcription inhibition by E. coli SspA

Wei, L., Yu, F.

(2020) Nucleic Acids Res 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C1D1E1F1G1 

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 - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 584.1 kDa 
• Atom Count: 35,049 
• Modelled Residue Count: 4,275 
• Deposited Residue Count: 4,990 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Stringent starvation protein A	B [auth I], C [auth J]	212	Escherichia coli	Mutation(s): 0  Gene Names: sspA EC: 2.5.1.18
UniProt
Find proteins for P0ACA3 (Escherichia coli (strain K12)) Explore P0ACA3  Go to UniProtKB:  P0ACA3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	D [auth K], E [auth A], F [auth B]	329	Escherichia coli	Mutation(s): 0  Gene Names: rpoA, ECPG_02615 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	G [auth C]	1,342	Escherichia coli K-12	Mutation(s): 1  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'	H [auth D]	1,407	Escherichia coli	Mutation(s): 0  Gene Names: rpoC EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7  Go to UniProtKB:  P0A8T7

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	I [auth E]	91	Escherichia coli	Mutation(s): 0  Gene Names: rpoZ EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800  Go to UniProtKB:  P0A800

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoD	J [auth F]	613	Escherichia coli	Mutation(s): 0  Gene Names: rpoD
UniProt
Find proteins for P00579 (Escherichia coli (strain K12)) Explore P00579  Go to UniProtKB:  P00579

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (63-mer)	A [auth H]	63	Escherichia coli

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (63-mer)	K [auth G]	63	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Lin, W., Feng, Y.

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-08-26
  Changes: Source and taxonomy
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references