9GE6 | pdb_00009ge6

Structure of E. coli YbbAP

PDB DOI: https://doi.org/10.2210/pdb9GE6/pdb
EM Map EMD-51291: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 141.78 kDa
Atom Count: 9,646
Modeled Residue Count: 1,247
Deposited Residue Count: 1,288
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P77504
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A9T8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

McAndrew, M.B.L.

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.