9KKB | pdb_00009kkb

Cryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens

• PDB DOI: https://doi.org/10.2210/pdb9KKB/pdb
• EM Map EMD-62384: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-13 Released: 2025-11-19 
• Deposition Author(s): Xiao, J., Wang, L., Wang, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens

Xiao, J., Wang, L.

(2025) mLife 

• DOI: https://doi.org/10.1002/mlf2.70052

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 64.79 kDa 
• Atom Count: 4,286 
• Modeled Residue Count: 530 
• Deposited Residue Count: 569 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdnG	A	407	Serratia marcescens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E2	B	162	Serratia marcescens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	C [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 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: 2025-11-19 
Deposition Author(s): Xiao, J., Wang, L., Wang, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release