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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
CitationJournal: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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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