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- PDB-9ge7: Structure of E. coli YbbAP with bound ATP analogue -

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Basic information

Entry
Database: PDB / ID: 9ge7
TitleStructure of E. coli YbbAP with bound ATP analogue
Components
  • Uncharacterized ABC transporter ATP-binding protein YbbA
  • Uncharacterized ABC transporter permease YbbP
KeywordsMEMBRANE PROTEIN / Type VII ABC transporter
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Membrane component of ABC transporter, predicted / : / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Membrane component of ABC transporter, predicted / : / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Uncharacterized ABC transporter ATP-binding protein YbbA / Uncharacterized ABC transporter permease YbbP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsMcAndrew, M.B.L. / Crow, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N014294/1 United Kingdom
Citation
Journal: PLoS Biol / Year: 2025
Title: Structural characterization of the YbbAP-TesA ABC transporter identifies it as a lipid hydrolase complex that extracts hydrophobic compounds from the bacterial inner membrane.
Authors: Martin B L McAndrew / Jonathan Cook / Amy Gill / Kavya Sahoo / Clare Thomas / Phillip J Stansfeld / Allister Crow /
Abstract: Type VII ABC transporters are ATP-powered membrane protein complexes that drive key biological processes in the bacterial cell envelope. In Escherichia coli, three of the four Type VII ABC systems ...Type VII ABC transporters are ATP-powered membrane protein complexes that drive key biological processes in the bacterial cell envelope. In Escherichia coli, three of the four Type VII ABC systems have been extensively characterized, including: the FtsEX-EnvC cell division complex, the LolCDE-LolA lipoprotein trafficking machinery, and the MacAB-TolC efflux pump. Here we describe a fourth E. coli Type VII ABC system, YbbAP-TesA, which combines a Type VII ABC transporter with a multifunctional hydrolytic enzyme. Structures of the complete YbbAP-TesA complex, and of YbbAP with and without bound ATP analogues, capture implied long-range transmembrane conformational changes that are the hallmark of this ABC superfamily's mechanotransmission mechanism. We further show that YbbAP-TesA can hydrolyze a variety of ester and thioester substrates and experimentally confirm a constellation of active site residues in TesA. Our data suggests YbbAP has a role in extracting hydrophobic molecules from the inner membrane and presenting these to TesA for hydrolysis. The work extends collective knowledge of the remarkable diversity of the ABC superfamily and establishes a new function for Type VII ABC transporters in bacterial cells.
#1: Journal: Biorxiv / Year: 2025
Title: Structure of YbbAP-TesA: a Type VII ABC transporter lipid-hydrolase complex
Authors: McAndrew, M.B. / Cook, J. / Gill, A. / Sahoo, K. / Thomas, C. / Stansfeld, P.J. / Crow, A.
History
DepositionAug 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ABC transporter permease YbbP
B: Uncharacterized ABC transporter ATP-binding protein YbbA
C: Uncharacterized ABC transporter ATP-binding protein YbbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8407
Polymers141,7793
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Uncharacterized ABC transporter permease YbbP


Mass: 89413.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Type VII ABC Transporter Transmembrane Protein YbbP
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ybbP, b0496, JW0485 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P77504
#2: Protein Uncharacterized ABC transporter ATP-binding protein YbbA


Mass: 26182.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Type VII ABC Transporter ATP-Binding Protein YbbA / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ybbA, b0495, JW0484 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0A9T8
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: YbbAP with bound ATP analogue / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.138362 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43(DE3)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameBuffer-ID
1150 mMsodium chloride1
220 mMHEPES1
30.005 %LMNG1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 50.80139123 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4093

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION5particle selectionbeta
7PHENIXmodel fitting
9PHENIXmodel refinement
12RELION5classificationbeta
13RELION53D reconstructionbeta
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 677670
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52834
Details: Map resolution of 3.66A reported by Phenix using masked FSC (half map 1,2) = 0.143. Mask smoothing radius is 7.30 A.
Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059956
ELECTRON MICROSCOPYf_angle_d0.63613526
ELECTRON MICROSCOPYf_dihedral_angle_d7.0411431
ELECTRON MICROSCOPYf_chiral_restr0.0381565
ELECTRON MICROSCOPYf_plane_restr0.0041728

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