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- PDB-9hkl: BetP-M150E in complex with GABA in an inward-facing state -

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Basic information

Entry
Database: PDB / ID: 9hkl
TitleBetP-M150E in complex with GABA in an inward-facing state
ComponentsGlycine betaine transporter BetP
KeywordsTRANSPORT PROTEIN / Glycine betaine transporter BetP
Function / homology
Function and homology information


symporter activity / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
BCCT transporter, conserved site / BCCT family of transporters signature. / BCCT transporter family / BCCT, betaine/carnitine/choline family transporter
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / CARDIOLIPIN / Chem-PGT / Glycine betaine transporter BetP
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsUrbansky, K. / Fu, L. / Madej, M.G. / Ziegler, C.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To be published
Title: Structural evidence for a link between substrate promiscuity and transport regulation in BetP mutants
Authors: Urbansky, K. / Gauthier-Manuel, L. / Fu, L. / Klinger, S. / Gaertner, R.M. / Madej, M.G. / Ziegler, C.
History
DepositionDec 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine betaine transporter BetP
B: Glycine betaine transporter BetP
C: Glycine betaine transporter BetP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,27510
Polymers195,8883
Non-polymers5,3877
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 Glycine betaine transporter BetP / Glycine betaine permease


Mass: 65296.008 Da / Num. of mol.: 3 / Mutation: M150E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: betP, Cgl0892, cg1016 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P54582
#2: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#3: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#4: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
Has ligand of interestN
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: Glycine betaine transporter BetP-M150E / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Source (recombinant)Organism: Escherichia coli DH5[alpha] (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
125 mMTRIS1
275 mMNaCl1
310 mMGamma-Amino-butanoic acid1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 52.66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1747020
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156949 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 4C7R

4c7r


Accession code: 4C7R / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.85 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412555
ELECTRON MICROSCOPYf_angle_d0.60217021
ELECTRON MICROSCOPYf_dihedral_angle_d14.9214408
ELECTRON MICROSCOPYf_chiral_restr0.041934
ELECTRON MICROSCOPYf_plane_restr0.0042075

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