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- PDB-9hjd: Cryo-EM structure of domperidone-bound human SLC19A3 in inward-op... -

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Basic information

Entry
Database: PDB / ID: 9hjd
TitleCryo-EM structure of domperidone-bound human SLC19A3 in inward-open state
Components
  • Nb3.3
  • Thiamine transporter 2
KeywordsMEMBRANE PROTEIN / Thiamine transporter / drug interaction / thiamine deficiency
Function / homology
Function and homology information


pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transmembrane transporter activity / thiamine transport / thiamine diphosphate biosynthetic process / transmembrane transport / membrane / plasma membrane
Similarity search - Function
Thiamine transporter 2 / Reduced folate carrier / Reduced folate carrier / MFS transporter superfamily
Similarity search - Domain/homology
: / Thiamine transporter 2
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsGabriel, F. / Loew, C.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structure-based discovery of inhibitors of the human SLC19A3
Authors: Gabriel, F. / Windshuegel, B. / Loew, C.
History
DepositionNov 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 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

Downloads & links

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Assembly

Deposited unit
B: Nb3.3
A: Thiamine transporter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5414
Polymers74,8932
Non-polymers6472
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: Antibody Nb3.3


Mass: 15205.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Thiamine transporter 2 / ThTr-2 / ThTr2 / Solute carrier family 19 member 3


Mass: 59687.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC19A3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZV2
#3: Chemical ChemComp-A1IVJ / 6-chloranyl-3-[1-[3-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)propyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one


Mass: 425.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: hSLC19A3:Nb3.3:domperidone / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 20 mM Tris-HCl, 150 mM NaCl, 0.002% LMNG, 0.0002% CHS, 0.25 mM domperidone
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 427625 / Symmetry type: POINT
RefinementResolution: 3.35→3.35 Å / Cor.coef. Fo:Fc: 0.473 / WRfactor Rwork: 0.521 / Average fsc free: 0 / Average fsc overall: 0.5236 / Average fsc work: 0.5236 / ESU R: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.5212 1725401 -
all0.521 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 39.364 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0124190
ELECTRON MICROSCOPYr_bond_other_d0.0020.0163931
ELECTRON MICROSCOPYr_angle_refined_deg1.4221.7935719
ELECTRON MICROSCOPYr_angle_other_deg0.7711.7018969
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.8555504
ELECTRON MICROSCOPYr_dihedral_angle_2_deg0.925518
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.29410632
ELECTRON MICROSCOPYr_dihedral_angle_6_deg17.34810171
ELECTRON MICROSCOPYr_chiral_restr0.0540.2646
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.024881
ELECTRON MICROSCOPYr_gen_planes_other0.0110.021073
ELECTRON MICROSCOPYr_nbd_refined0.2340.21161
ELECTRON MICROSCOPYr_symmetry_nbd_other0.2220.23877
ELECTRON MICROSCOPYr_nbtor_refined0.2130.22222
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0860.22248
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1690.265
ELECTRON MICROSCOPYr_mcbond_it042025
ELECTRON MICROSCOPYr_mcbond_other042025
ELECTRON MICROSCOPYr_mcangle_it07.1732526
ELECTRON MICROSCOPYr_mcangle_other07.1732527
ELECTRON MICROSCOPYr_scbond_it042165
ELECTRON MICROSCOPYr_scbond_other042166
ELECTRON MICROSCOPYr_scangle_it07.3653193
ELECTRON MICROSCOPYr_scangle_other07.3653194
ELECTRON MICROSCOPYr_lrange_it047.59217131
ELECTRON MICROSCOPYr_lrange_other047.59117132
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
3.4-3.4880.7031279960.7031279960.180.703
3.488-3.5840.6351245250.6351245250.2510.635
3.584-3.6880.5831202720.5831202720.3290.583
3.688-3.8010.5351178290.5351178290.3980.535
3.801-3.9260.4981139660.4981139660.4740.498
3.926-4.0640.4841102450.4841102450.5550.484
4.064-4.2170.4871067090.4871067090.630.487
4.217-4.3890.4911020530.4911020530.6810.491
4.389-4.5840.49978490.49978490.7020.49
4.584-4.8080.492942230.492942230.7070.492
4.808-5.0680.486892760.486892760.6870.486
5.068-5.3760.475840230.475840230.6390.475
5.376-5.7470.474794840.474794840.5550.474
5.747-6.2070.49737820.49737820.4920.49
6.207-6.7990.509677570.509677570.5010.509
6.799-7.6010.507612990.507612990.5860.507
7.601-8.7760.513541750.513541750.6830.513
8.776-10.7460.533457350.533457350.7630.533
10.746-15.1890.687352430.687352430.7890.687
15.189-318.720.837193200.837193200.5590.837

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