9NP6 | pdb_00009np6

Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA

• PDB DOI: https://doi.org/10.2210/pdb9NP6/pdb
• NAKB: 9NP6
• EM Map EMD-49626: EMDB EMDataResource

• Classification: ISOMERASE/DNA
• Organism(s): Mycolicibacterium smegmatis MC2 155, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2025-03-11 Released: 2025-03-19 
• Deposition Author(s): Warren, G.M., De la Cruz, M.J., Goldgur, Y., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of an initiation complex mycobacterial helicase-nuclease AdnAB at a blunt double-strand break reveals locl melting that engages the 3' tracking strand at the ratchet pawl of the helicase motor

Warren, G.M., De la Cruz, M.J., Goldgur, Y., Meir, A., Greene, E.C., Shuman, S.

To be published.

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: 248.55 kDa 
• Atom Count: 12,400 
• Modeled Residue Count: 1,679 
• Deposited Residue Count: 2,200 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA 3'-5' helicase	A	1,046	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_1941 EC: 5.6.2.4
UniProt
Find proteins for A0QTR9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTR9  Go to UniProtKB:  A0QTR9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA 3'-5' helicase	B	1,095	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEI_1900 EC: 5.6.2.4
UniProt
Find proteins for I7FZ56 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7FZ56  Go to UniProtKB:  I7FZ56

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (30-MER)	C [auth X]	59	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	D [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)	E [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Warren, G.M., De la Cruz, M.J., Goldgur, Y., Shuman, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release