8XA8 | pdb_00008xa8

Cryo-EM structure of Bacillus RNAP and HelD complex

• PDB DOI: https://doi.org/10.2210/pdb8XA8/pdb
• EM Map EMD-38197: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Bacillus
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2023-12-02 Released: 2024-12-04 
• Deposition Author(s): Chen, M., Jin, Q., Yuan, S., Liu, B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A phage encoded sigA-dependent transcription inhibitor also attacks host HelD-mediated defence system

Chen, M., Jin, Q., Zhang, K., Wang, Y., Chen, H., Yu, Z., Matthews, S., Yuan, S., Liu, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B1C1D1E1F1G1 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 464.65 kDa 
• Atom Count: 28,991 
• Modeled Residue Count: 3,723 
• Deposited Residue Count: 4,103 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	314	Bacillus	Mutation(s): 0  Gene Names: rpoA EC: 2.7.7.6
UniProt
Find proteins for P20429 (Bacillus subtilis (strain 168)) Explore P20429  Go to UniProtKB:  P20429

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	C [auth D]	1,199	Bacillus	Mutation(s): 0  Gene Names: rpoC EC: 2.7.7.6
UniProt
Find proteins for P37871 (Bacillus subtilis (strain 168)) Explore P37871  Go to UniProtKB:  P37871

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit epsilon	D [auth E]	69	Bacillus	Mutation(s): 1  Gene Names: rnpZA EC: 2.7.7.6
UniProt
Find proteins for O31718 (Bacillus subtilis (strain 168)) Explore O31718  Go to UniProtKB:  O31718

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E [auth F]	67	Bacillus	Mutation(s): 0  Gene Names: rpoZ EC: 2.7.7.6
UniProt
Find proteins for O35011 (Bacillus subtilis (strain 168)) Explore O35011  Go to UniProtKB:  O35011

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase IV	F [auth H]	774	Bacillus	Mutation(s): 0  Gene Names: helD EC: 3.6.4.12
UniProt
Find proteins for O32215 (Bacillus subtilis (strain 168)) Explore O32215  Go to UniProtKB:  O32215

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	G [auth C]	1,193	Bacillus	Mutation(s): 0  Gene Names: rpoB EC: 2.7.7.6
UniProt
Find proteins for P37870 (Bacillus subtilis (strain 168)) Explore P37870  Go to UniProtKB:  P37870

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit delta	H [auth I]	173	Bacillus	Mutation(s): 0  Gene Names: rpoE
UniProt
Find proteins for P12464 (Bacillus subtilis (strain 168)) Explore P12464  Go to UniProtKB:  P12464

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Chen, M., Jin, Q., Yuan, S., Liu, B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270151
National Natural Science Foundation of China (NSFC)	China	32270172

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Data collection