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- PDB-9hko: Downregulated closed state of BetP in complex with betaine -

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Basic information

Entry
Database: PDB / ID: 9hko
TitleDownregulated closed state of BetP in complex with betaine
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
TRIMETHYL GLYCINE / Chem-PGT / Glycine betaine transporter BetP
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsUrbansky, K. / Fu, L. / Madej, M.G. / Ziegler, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: To be published
Title: Transport regulation of BetP
Authors: Heinz, V. / Gueler, G. / Urbansky, K. / Fu, L. / Madej, M.G. / Maksimov, S. / Hamdi, F. / Kastritis, P.L. / Maentele, W. / Kapiki, D. / Cordes, T. / Kraemer, R. / Perez, C. / 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)198,54811
Polymers195,8943
Non-polymers2,6548
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: 65298.094 Da / Num. of mol.: 3
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-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
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
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 / 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 mMtrimethyl glycine1
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
Image recordingElectron dose: 61.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2078666
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 263206 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4C7R

4c7r


Accession code: 4C7R / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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