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- EMDB-52738: Upregulated state of BetP with Potassium in Amphipol A8-35 -

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Basic information

Entry
Database: EMDB / ID: EMD-52738
TitleUpregulated state of BetP with Potassium in Amphipol A8-35
Map data
Sample
  • Complex: Glycine betaine transporter BetP
    • Protein or peptide: Glycine betaine transporter BetP
  • Ligand: POTASSIUM ION
KeywordsGlycine betaine transporter BetP / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsUrbansky K / Fu L / Madej MG / Ziegler C
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: To be published
Title: Transport regulation of BetP
Authors: Heinz V / Gueler G / Urbansky K / Fu L / Madej MG / Maksimov S / Hamdi F / Kastritis PL / Maentele W / Kapiki D / Cordes T / Kraemer R / Perez C / Ziegler C
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52738.png

Downloads & links

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Map

FileDownload / File: emd_52738.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 360 pix.
= 284.076 Å		0.79 Å/pix.
x 360 pix.
= 284.076 Å		0.79 Å/pix.
x 360 pix.
= 284.076 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7891 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.4085318 - 0.56719905
Average (Standard dev.)0.00029103938 (±0.012277803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 284.076 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52738_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52738_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glycine betaine transporter BetP

EntireName: Glycine betaine transporter BetP
Components
  • Complex: Glycine betaine transporter BetP
    • Protein or peptide: Glycine betaine transporter BetP
  • Ligand: POTASSIUM ION

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Supramolecule #1: Glycine betaine transporter BetP

SupramoleculeName: Glycine betaine transporter BetP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Corynebacterium glutamicum (bacteria)

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Macromolecule #1: Glycine betaine transporter BetP

MacromoleculeName: Glycine betaine transporter BetP / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 65.525242 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: WSHPQFEKGA ETTTSDPNPK PIVEDAQPEQ ITATEELAGL LENPTNLEGK LADAEEEIIL EGEDTQASLN WSVIVPALVI VLATVVWGI GFKDSFTNFA SSALSAVVDN LGWAFILFGT VFVFFIVVIA ASKFGTIRLG RIDEAPEFRT VSWISMMFAA G MGIGLMFY ...String:
WSHPQFEKGA ETTTSDPNPK PIVEDAQPEQ ITATEELAGL LENPTNLEGK LADAEEEIIL EGEDTQASLN WSVIVPALVI VLATVVWGI GFKDSFTNFA SSALSAVVDN LGWAFILFGT VFVFFIVVIA ASKFGTIRLG RIDEAPEFRT VSWISMMFAA G MGIGLMFY GTTEPLTFYR NGVPGHDEHN VGVAMSTTMF HWTLHPWAIY AIVGLAIAYS TFRVGRKQLL SSAFVPLIGE KG AEGWLGK LIDILAIIAT VFGTACSLGL GALQIGAGLS AANIIEDPSD WTIVGIVSVL TLAFIFSAIS GVGKGIQYLS NAN MVLAAL LAIFVFVVGP TVSILNLLPG SIGNYLSNFF QMAGRTAMSA DGTAGEWLGS WTIFYWAWWI SWSPFVGMFL ARIS RGRSI REFILGVLLV PAGVSTVWFS IFGGTAIVFE QNGESIWGDG AAEEQLFGLL HALPGGQIMG IIAMILLGTF FITSA DSAS TVMGTMSQHG QLEANKWVTA AWGVATAAIG LTLLLSGGDN ALSNLQNVTI VAATPFLFVV IGLMFALVKD LSNDVI YLE YREQQRFNAR LARERRVHNE HRKRELAAKR RRERKASGAG KRR

UniProtKB: Glycine betaine transporter BetP

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
25.0 mMTRIS
75.0 mMNaCl
10.0 mMtrimethyl glycine
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 53.07 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91156
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9i5z


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9i8u:
Upregulated state of BetP with Potassium in Amphipol A8-35

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