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- EMDB-51422: BetP heterotrimeric complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51422
TitleBetP heterotrimeric complex
Map data
Sample
  • Complex: Glycine Betaine Transporter BetP Heterotrimer
    • Protein or peptide: Glycine betaine transporter BetP
  • Ligand: SODIUM ION
  • Ligand: TRIMETHYL GLYCINE
  • Ligand: dodecyl beta-D-glucopyranoside
  • Ligand: CARDIOLIPIN
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water
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: 3.04 Å
AuthorsUrbansky K / Fu L / Madej MG / Ziegler C
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To be published
Title: Structure of Glycine betaine transporter BetP heterotrimeric complex
Authors: Urbansky K / Fu L / Madej MG / Ziegler C
History
DepositionAug 25, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51422.png

Downloads & links

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Map

FileDownload / File: emd_51422.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: 0.18
Minimum - Maximum-1.4098887 - 2.3146305
Average (Standard dev.)0.0013399369 (±0.046996847)
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_51422_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_51422_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 Heterotrimer

EntireName: Glycine Betaine Transporter BetP Heterotrimer
Components
  • Complex: Glycine Betaine Transporter BetP Heterotrimer
    • Protein or peptide: Glycine betaine transporter BetP
  • Ligand: SODIUM ION
  • Ligand: TRIMETHYL GLYCINE
  • Ligand: dodecyl beta-D-glucopyranoside
  • Ligand: CARDIOLIPIN
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: Glycine Betaine Transporter BetP Heterotrimer

SupramoleculeName: Glycine Betaine Transporter BetP Heterotrimer / 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
Details: >chainA: N-terminal StrepII, R584C WSHPQFEKMTTSDPNPKPIVEDAQPEQITATEELAGLLENPTNLEGKLADAEEEIILEGEDTQASLNW SVIVPALVIVLATVVWGIGFKDSFTNFASSALSAVVDNLGWAFILFGTVFVFFIVVIAAS ...Details: >chainA: N-terminal StrepII, R584C WSHPQFEKMTTSDPNPKPIVEDAQPEQITATEELAGLLENPTNLEGKLADAEEEIILEGEDTQASLNW SVIVPALVIVLATVVWGIGFKDSFTNFASSALSAVVDNLGWAFILFGTVFVFFIVVIAAS KFGTIRLGRIDEAPEFRTVSWISMMFAAGMGIGLMFYGTTEPLTFYRNGVPGHDEHNVGV AMSTTMFHWTLHPWAIYAIVGLAIAYSTFRVGRKQLLSSAFVPLIGEKGAEGWLGKLIDI LAIIATVFGTACSLGLGALQIGAGLSAANIIEDPSDWTIVGIVSVLTLAFIFSAISGVGK GIQYLSNANMVLAALLAIFVFVVGPTVSILNLLPGSIGNYLSNFFQMAGRTAMSADGTAG EWLGSWTIFYWAWWISWSPFVGMFLARISRGRSIREFILGVLLVPAGVSTVWFSIFGGTA IVFEQNGESIWGDGAAEEQLFGLLHALPGGQIMGIIAMILLGTFFITSADSASTVMGTMS QHGQLEANKWVTAAWGVATAAIGLTLLLSGGDNALSNLQNVTIVAATPFLFVVIGLMFAL VKDLSNDVIYLEYREQQRFNARLARERRVHNEHRKRELAAKRRCERKASGAGKRR >chainB: N-terminal StrepII, delC12, C-terminal His WSHPQFEKMTTSDPNPKPIVEDAQPEQITATEELAGLLENPTNLEGKLADAEEEIILEGEDTQASLNW SVIVPALVIVLATVVWGIGFKDSFTNFASSALSAVVDNLGWAFILFGTVFVFFIVVIAAS KFGTIRLGRIDEAPEFRTVSWISMMFAAGMGIGLMFYGTTEPLTFYRNGVPGHDEHNVGV AMSTTMFHWTLHPWAIYAIVGLAIAYSTFRVGRKQLLSSAFVPLIGEKGAEGWLGKLIDI LAIIATVFGTACSLGLGALQIGAGLSAANIIEDPSDWTIVGIVSVLTLAFIFSAISGVGK GIQYLSNANMVLAALLAIFVFVVGPTVSILNLLPGSIGNYLSNFFQMAGRTAMSADGTAG EWLGSWTIFYWAWWISWSPFVGMFLARISRGRSIREFILGVLLVPAGVSTVWFSIFGGTA IVFEQNGESIWGDGAAEEQLFGLLHALPGGQIMGIIAMILLGTFFITSADSASTVMGTMS QHGQLEANKWVTAAWGVATAAIGLTLLLSGGDNALSNLQNVTIVAATPFLFVVIGLMFAL VKDLSNDVIYLEYREQQRFNARLARERRVHNEHRKRELAAKRRHHHHHH >chainC: N-terminal StrepII, E25C, delC12, C-terminal Flag WSHPQFEKMTTSDPNPKPIVEDAQPEQITATECLAGLLENPTNLEGKLADAEEEIILEGEDTQASLNW SVIVPALVIVLATVVWGIGFKDSFTNFASSALSAVVDNLGWAFILFGTVFVFFIVVIAAS KFGTIRLGRIDEAPEFRTVSWISMMFAAGMGIGLMFYGTTEPLTFYRNGVPGHDEHNVGV AMSTTMFHWTLHPWAIYAIVGLAIAYSTFRVGRKQLLSSAFVPLIGEKGAEGWLGKLIDI LAIIATVFGTACSLGLGALQIGAGLSAANIIEDPSDWTIVGIVSVLTLAFIFSAISGVGK GIQYLSNANMVLAALLAIFVFVVGPTVSILNLLPGSIGNYLSNFFQMAGRTAMSADGTAG EWLGSWTIFYWAWWISWSPFVGMFLARISRGRSIREFILGVLLVPAGVSTVWFSIFGGTA IVFEQNGESIWGDGAAEEQLFGLLHALPGGQIMGIIAMILLGTFFITSADSASTVMGTMS QHGQLEANKWVTAAWGVATAAIGLTLLLSGGDNALSNLQNVTIVAATPFLFVVIGLMFAL VKDLSNDVIYLEYREQQRFNARLARERRVHNEHRKRELAAKRRDYKDDDK
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 65.244039 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: WSHPQFEKMT TSDPNPKPIV EDAQPEQITA TEELAGLLEN PTNLEGKLAD AEEEIILEGE DTQASLNWSV IVPALVIVLA TVVWGIGFK DSFTNFASSA LSAVVDNLGW AFILFGTVFV FFIVVIAASK FGTIRLGRID EAPEFRTVSW ISMMFAAGMG I GLMFYGTT ...String:
WSHPQFEKMT TSDPNPKPIV EDAQPEQITA TEELAGLLEN PTNLEGKLAD AEEEIILEGE DTQASLNWSV IVPALVIVLA TVVWGIGFK DSFTNFASSA LSAVVDNLGW AFILFGTVFV FFIVVIAASK FGTIRLGRID EAPEFRTVSW ISMMFAAGMG 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 RELAAKRRCE RKASGAGKRR

UniProtKB: Glycine betaine transporter BetP

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: TRIMETHYL GLYCINE

MacromoleculeName: TRIMETHYL GLYCINE / type: ligand / ID: 3 / Number of copies: 3 / Formula: BET
Molecular weightTheoretical: 118.154 Da
Chemical component information

ChemComp-BET:
TRIMETHYL GLYCINE

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Macromolecule #4: dodecyl beta-D-glucopyranoside

MacromoleculeName: dodecyl beta-D-glucopyranoside / type: ligand / ID: 4 / Number of copies: 2 / Formula: XKJ
Molecular weightTheoretical: 348.475 Da
Chemical component information

ChemComp-XKJ:
dodecyl beta-D-glucopyranoside

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Macromolecule #5: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #6: (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: 6 / Number of copies: 2 / 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 #7: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 7 / 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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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 100 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
TemperatureMin: 96.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3929 / Average exposure time: 5.88 sec. / Average electron dose: 53.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1509120
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274359
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-9gkk:
BetP heterotrimeric complex

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