9GE7 | pdb_00009ge7

Structure of E. coli YbbAP with bound ATP analogue

• PDB DOI: https://doi.org/10.2210/pdb9GE7/pdb
• EM Map EMD-51292: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-07 Released: 2025-05-28 
• Deposition Author(s): McAndrew, M.B.L., Crow, A.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure of YbbAP-TesA: a Type VII ABC transporter lipid-hydrolase complex

McAndrew, M.B., Cook, J., Gill, A., Sahoo, K., Thomas, C., Stansfeld, P.J., Crow, A.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.05.16.654284

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 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: 142.84 kDa 
• Atom Count: 9,773 
• Modeled Residue Count: 1,256 
• Deposited Residue Count: 1,288 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized ABC transporter permease YbbP	A	804	Escherichia coli K-12	Mutation(s): 0  Gene Names: ybbP, b0496, JW0485
UniProt
Find proteins for P77504 (Escherichia coli (strain K12)) Explore P77504  Go to UniProtKB:  P77504

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized ABC transporter ATP-binding protein YbbA	B, C	242	Escherichia coli K-12	Mutation(s): 0  Gene Names: ybbA, b0495, JW0484
UniProt
Find proteins for P0A9T8 (Escherichia coli (strain K12)) Explore P0A9T8  Go to UniProtKB:  P0A9T8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	D [auth B], F [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	E [auth B], G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	5

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): McAndrew, M.B.L., Crow, A.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N014294/1

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release