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- PDB-9i5z: Upregulated state of BetP in potassium -

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Basic information

Entry
Database: PDB / ID: 9i5z
TitleUpregulated state of BetP in potassium
ComponentsGlycine betaine transporter BetP
KeywordsTRANSPORT PROTEIN / Glycine betaine transporter BetP
Function / homologyBCCT transporter, conserved site / BCCT family of transporters signature. / BCCT transporter family / BCCT, betaine/carnitine/choline family transporter / symporter activity / metal ion binding / identical protein binding / plasma membrane / Glycine betaine transporter BetP
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsUrbansky, K. / Fu, L. / Madej, M.G. / Horn, G. / Ziegler, C.
Funding support1items
OrganizationGrant numberCountry
Other government
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
DepositionJan 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data 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


Theoretical massNumber of molelcules
Total (without water)195,8943
Polymers195,8943
Non-polymers00
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
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: all / 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
3300 mMKCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 57 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
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 456000 / Symmetry type: POINT
RefinementHighest resolution: 3.09 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411585
ELECTRON MICROSCOPYf_angle_d0.54915795
ELECTRON MICROSCOPYf_dihedral_angle_d4.5191548
ELECTRON MICROSCOPYf_chiral_restr0.0361852
ELECTRON MICROSCOPYf_plane_restr0.0041934

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