9GE8 | pdb_00009ge8

Structure of E. coli YbbAP-TesA with bound ATP analogue

• PDB DOI: https://doi.org/10.2210/pdb9GE8/pdb
• EM Map EMD-51293: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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: 4.55 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 4-mer - A2B1C1 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: 163.31 kDa 
• Atom Count: 11,130 
• Modeled Residue Count: 1,426 
• Deposited Residue Count: 1,470 
• Unique protein chains: 3

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase 1/protease 1/lysophospholipase L1	D [auth T]	182	Escherichia coli K-12	Mutation(s): 1  Gene Names: tesA, apeA, pldC, b0494, JW0483 EC: 3.1.2.2 (PDB Primary Data), 3.1.1.2 (PDB Primary Data), 3.1.1.5 (PDB Primary Data), 3.1.2.14 (PDB Primary Data), 3.4.21 (PDB Primary Data)
UniProt
Find proteins for P0ADA1 (Escherichia coli (strain K12)) Explore P0ADA1  Go to UniProtKB:  P0ADA1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

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