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- EMDB-52232: Transient activated state of BetP-M150E -

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Basic information

Entry
Database: EMDB / ID: EMD-52232
TitleTransient activated state of BetP-M150E
Map data
Sample
  • Complex: Glycine betaine transporter BetP-M150E
    • Protein or peptide: Glycine betaine transporter BetP
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: DODECYL-BETA-D-MALTOSIDE
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: 2.74 Å
AuthorsUrbansky K / Gauthier-Manuel L / Fu L / Madej MG / Ziegler C
Funding support1 items
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 / Fu L / Klinger S / Madej MG / Ziegler C
History
DepositionDec 3, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52232.png

Downloads & links

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Map

FileDownload / File: emd_52232.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 252.512 Å		0.79 Å/pix.
x 320 pix.
= 252.512 Å		0.79 Å/pix.
x 320 pix.
= 252.512 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: 0.226
Minimum - Maximum-1.7594999 - 2.210148
Average (Standard dev.)0.0017558581 (±0.054314695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 252.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52232_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_52232_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-M150E

EntireName: Glycine betaine transporter BetP-M150E
Components
  • Complex: Glycine betaine transporter BetP-M150E
    • Protein or peptide: Glycine betaine transporter BetP
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Glycine betaine transporter BetP-M150E

SupramoleculeName: Glycine betaine transporter BetP-M150E / 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: 65.296008 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: WSHPQFEKMT TSDPNPKPIV EDAQPEQITA TEELAGLLEN PTNLEGKLAD AEEEIILEGE DTQASLNWSV IVPALVIVLA TVVWGIGFK DSFTNFASSA LSAVVDNLGW AFILFGTVFV FFIVVIAASK FGTIRLGRID EAPEFRTVSW ISMMFAAGEG I GLMFYGTT ...String:
WSHPQFEKMT TSDPNPKPIV EDAQPEQITA TEELAGLLEN PTNLEGKLAD AEEEIILEGE DTQASLNWSV IVPALVIVLA TVVWGIGFK DSFTNFASSA LSAVVDNLGW AFILFGTVFV FFIVVIAASK FGTIRLGRID EAPEFRTVSW ISMMFAAGEG I GLMFYGTT EPLTFYRNGV PGHDEHNVGV AMSTTMFHWT LHPWAIYAIV GLAIAYSTFR VGRKQLLSSA FVPLIGEKGA EG WLGKLID ILAIIATVFG TACSLGLGAL QIGAGLSAAN IIEDPSDWTI VGIVSVLTLA FIFSAISGVG KGIQYLSNAN MVL AALLAI FVFVVGPTVS ILNLLPGSIG NYLSNFFQMA GRTAMSADGT AGEWLGSWTI FYWAWWISWS PFVGMFLARI SRGR SIREF ILGVLLVPAG VSTVWFSIFG GTAIVFEQNG ESIWGDGAAE EQLFGLLHAL PGGQIMGIIA MILLGTFFIT SADSA STVM GTMSQHGQLE ANKWVTAAWG VATAAIGLTL LLSGGDNALS NLQNVTIVAA TPFLFVVIGL MFALVKDLSN DVIYLE YRE QQRFNARLAR ERRVHNEHRK RELAAKRRRE RKASGAGKRR

UniProtKB: Glycine betaine transporter BetP

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Macromolecule #2: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 2 / Number of copies: 3 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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Macromolecule #3: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

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Macromolecule #4: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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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 mMGamma-amino-butanoic acid
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: 52.66 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
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1747020
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213809
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:

4c7r


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9hkm:
Transient activated state of BetP-M150E

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