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- PDB-9gkk: BetP heterotrimeric complex -

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Basic information

Entry
Database: PDB / ID: 9gkk
TitleBetP heterotrimeric complex
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 / CARDIOLIPIN / Chem-PGT / dodecyl beta-D-glucopyranoside / Glycine betaine transporter BetP
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsUrbansky, K. / Fu, L. / Madej, M.G. / Ziegler, C.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To be published
Title: Structure of Glycine betaine transporter BetP heterotrimeric complex
Authors: Urbansky, K. / Fu, L. / Madej, M.G. / Ziegler, C.
History
DepositionAug 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 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)200,32915
Polymers195,7323
Non-polymers4,59712
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 57 - 565 / Label seq-ID: 65 - 573

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
211BB
322AA
422CC
533BB
633CC

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glycine betaine transporter BetP / Glycine betaine permease


Mass: 65244.039 Da / Num. of mol.: 3 / Mutation: chain A R584C, chain C E25C
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: betP, Cgl0892, cg1016 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P54582

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Sugars , 2 types, 3 molecules

#4: Sugar ChemComp-XKJ / dodecyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 348.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O6
#7: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12NO2
#5: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: 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.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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 Heterotrimer / 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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 magnification: 60000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (min): 96 K
Image recordingAverage exposure time: 5.88 sec. / Electron dose: 53.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3929
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 49

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1509120
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274359 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 4C7R

4c7r


Accession code: 4C7R / Source name: PDB / Type: experimental model
RefinementResolution: 3.04→3.04 Å / Cor.coef. Fo:Fc: 0.655 / WRfactor Rwork: 0.437 / SU B: 26.373 / SU ML: 0.445 / Average fsc free: 0 / Average fsc overall: 0.8291 / Average fsc work: 0.8291 / ESU R: 0.691
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.4373 92324 -
all0.437 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 51.264 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01212168
ELECTRON MICROSCOPYr_bond_other_d00.01611848
ELECTRON MICROSCOPYr_angle_refined_deg1.3311.74916538
ELECTRON MICROSCOPYr_angle_other_deg0.4371.68127091
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.06351521
ELECTRON MICROSCOPYr_dihedral_angle_2_deg16.899553
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.77101789
ELECTRON MICROSCOPYr_dihedral_angle_6_deg15.22710435
ELECTRON MICROSCOPYr_chiral_restr0.0580.21921
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0214104
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022920
ELECTRON MICROSCOPYr_nbd_refined0.2320.23418
ELECTRON MICROSCOPYr_symmetry_nbd_other0.2040.211096
ELECTRON MICROSCOPYr_nbtor_refined0.20.26470
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0730.26515
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1940.2143
ELECTRON MICROSCOPYr_metal_ion_refined0.2330.22
ELECTRON MICROSCOPYr_mcbond_it3.1384.9076105
ELECTRON MICROSCOPYr_mcbond_other3.1394.9116096
ELECTRON MICROSCOPYr_mcangle_it5.398.8037619
ELECTRON MICROSCOPYr_mcangle_other5.3938.8087614
ELECTRON MICROSCOPYr_scbond_it3.5675.5326063
ELECTRON MICROSCOPYr_scbond_other3.5675.5326064
ELECTRON MICROSCOPYr_scangle_it6.3869.9048919
ELECTRON MICROSCOPYr_scangle_other6.3869.9038920
ELECTRON MICROSCOPYr_lrange_it13.3256.32250505
ELECTRON MICROSCOPYr_lrange_other13.3256.32250506
ELECTRON MICROSCOPYr_ncsr_local_group_10.1570.0515177
ELECTRON MICROSCOPYr_ncsr_local_group_20.1780.0514557
ELECTRON MICROSCOPYr_ncsr_local_group_30.1770.0514620
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.156520.05006
12BELECTRON MICROSCOPYLocal ncs0.156520.05006
23AELECTRON MICROSCOPYLocal ncs0.177780.05006
24CELECTRON MICROSCOPYLocal ncs0.177780.05006
35BELECTRON MICROSCOPYLocal ncs0.177340.05006
36CELECTRON MICROSCOPYLocal ncs0.177340.05006
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.07-3.151.58669341.58669340.5511.586
3.15-3.2361.03565991.03565990.651.035
3.236-3.330.72764940.72764940.7350.727
3.33-3.4320.48562550.48562550.7830.485
3.432-3.5450.35460820.35460820.8210.354
3.545-3.6690.33359230.33359230.8720.333
3.669-3.8070.36256660.36256660.90.362
3.807-3.9630.36654430.36654430.9110.366
3.963-4.1390.37952640.37952640.9180.379
4.139-4.340.36750100.36750100.9260.367
4.34-4.5750.36147700.36147700.9230.361
4.575-4.8520.33944990.33944990.9250.339
4.852-5.1860.30442190.30442190.9050.304
5.186-5.6010.2939590.2939590.8880.29
5.601-6.1340.36436530.36436530.8520.364
6.134-6.8560.49932620.49932620.8320.499
6.856-7.9130.46928980.46928980.8450.469
7.913-9.6810.42224360.42224360.8980.422
9.681-13.6490.57919170.57919170.9020.579
13.649-123.11.0910401.0910400.9561.09

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