8WLD | pdb_00008wld

Cryo-EM structure of SIR2/HerA antiphage complex

• PDB DOI: https://doi.org/10.2210/pdb8WLD/pdb
• EM Map EMD-37616: EMDB EMDataResource

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


• Deposited: 2023-09-29 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: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of SIR2/HerA antiphage complex

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 15-mer - A9B5C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A9B6 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - B5 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 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: 858.24 kDa 
• Atom Count: 48,292 
• Modeled Residue Count: 6,850 
• Deposited Residue Count: 7,605 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIR2-like domain-containing protein	A [auth S], B [auth T], C [auth K], D [auth J], E [auth R], F [auth P], G [auth Q], N [auth H], O [auth E]	381	Paenibacillus sp. 453mf	Mutation(s): 0  Gene Names: SAMN04488601_104157

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase HerA central domain-containing protein	H [auth O], I [auth A], J [auth D], K [auth L], L [auth M], M [auth N]	696	Paenibacillus sp. 453mf	Mutation(s): 0  Gene Names: SAMN04488601_104156

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.48 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