8WIV | pdb_00008wiv

Cryo-EM structure of a bacterial protein

• PDB DOI: https://doi.org/10.2210/pdb8WIV/pdb
• EM Map EMD-37569: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Paenibacillus sp. 453mf
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-25 Released: 2024-09-11 
• Deposition Author(s): Yu, G., Liao, F., Li, X., Li, Z., Zhang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a bacterial protein

Yu, G., Liao, F., Li, X., Li, Z., Zhang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 390.32 kDa 
• Atom Count: 22,622 
• Modeled Residue Count: 2,944 
• Deposited Residue Count: 3,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase HerA central domain-containing protein	A, B [auth D], C [auth M], D [auth O], E [auth L]	696	Paenibacillus sp. 453mf	Mutation(s): 0  Gene Names: SAMN04488601_104156

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS (Subject of Investigation/LOI)	G [auth D], H [auth M], J [auth O], L	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG	F [auth D], I [auth M], K [auth O], M [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 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: 2024-09-11 
Deposition Author(s): Yu, G., Liao, F., Li, X., Li, Z., Zhang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200496

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Data collection, Derived calculations