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- EMDB-52213: Cryo-EM structure of domperidone-bound human SLC19A3 in inward-op... -

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Basic information

Entry
Database: EMDB / ID: EMD-52213
TitleCryo-EM structure of domperidone-bound human SLC19A3 in inward-open state
Map data
Sample
  • Complex: hSLC19A3:Nb3.3:domperidone
    • Protein or peptide: Nb3.3
    • Protein or peptide: Thiamine transporter 2
  • Ligand: 6-chloranyl-3-[1-[3-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)propyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsThiamine transporter / drug interaction / thiamine deficiency / MEMBRANE PROTEIN
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 speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsGabriel F / Loew C
Funding support1 items
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, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52213.png

Downloads & links

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Map

FileDownload / File: emd_52213.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-6.531221 - 7.6340175
Average (Standard dev.)-0.0011267402 (±0.06283112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52213_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52213_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52213_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : hSLC19A3:Nb3.3:domperidone

EntireName: hSLC19A3:Nb3.3:domperidone
Components
  • Complex: hSLC19A3:Nb3.3:domperidone
    • Protein or peptide: Nb3.3
    • Protein or peptide: Thiamine transporter 2
  • Ligand: 6-chloranyl-3-[1-[3-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)propyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: hSLC19A3:Nb3.3:domperidone

SupramoleculeName: hSLC19A3:Nb3.3:domperidone / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nb3.3

MacromoleculeName: Nb3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.205778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQAGDSLRL SCAASGRTFS NYYMAWFRQA PGKEREFVAA IRLSYGSTYY ADSVRGRFTI SKDNAKNTVN LRMNSLKSE DTAIYYCAAA EDRWALAVRT ATTYNYWGQG TQVTVSSHHH HHHEPEA

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Macromolecule #2: Thiamine transporter 2

MacromoleculeName: Thiamine transporter 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.687609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDCYRTSLSS SWIYPTVILC LFGFFSMMRP SEPFLIPYLS GPDKNLTSAE ITNEIFPVWT YSYLVLLLPV FVLTDYVRYK PVIILQGIS FIITWLLLLF GQGVKTMQVV EFFYGMVTAA EVAYYAYIYS VVSPEHYQRV SGYCRSVTLA AYTAGSVLAQ L LVSLANMS ...String:
MDCYRTSLSS SWIYPTVILC LFGFFSMMRP SEPFLIPYLS GPDKNLTSAE ITNEIFPVWT YSYLVLLLPV FVLTDYVRYK PVIILQGIS FIITWLLLLF GQGVKTMQVV EFFYGMVTAA EVAYYAYIYS VVSPEHYQRV SGYCRSVTLA AYTAGSVLAQ L LVSLANMS YFYLNVISLA SVSVAFLFSL FLPMPKKSMF FHAKPSREIK KSSSVNPVLE ETHEGEAPGC EEQKPTSEIL ST SGKLNKG QLNSLKPSNV TVDVFVQWFQ DLKECYSSKR LFYWSLWWAF ATAGFNQVLN YVQILWDYKA PSQDSSIYNG AVE AIATFG GAVAAFAVGY VKVNWDLLGE LALVVFSVVN AGSLFLMHYT ANIWACYAGY LIFKSSYMLL ITIAVFQIAV NLNV ERYAL VFGINTFIAL VIQTIMTVIV VDQRGLNLPV SIQFLVYGSY FAVIAGIFLM RSMYITYSTK SQKDVQSPAP SENPD VSHP EEESNIIMST KLLEVLFQGP SSGWSHPQFE KGGGSGGGSG GSAWSHPQFE K

UniProtKB: Thiamine transporter 2

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Macromolecule #3: 6-chloranyl-3-[1-[3-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)prop...

MacromoleculeName: 6-chloranyl-3-[1-[3-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)propyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1IVJ
Molecular weightTheoretical: 425.911 Da

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4
Details: 20 mM Tris-HCl, 150 mM NaCl, 0.002% LMNG, 0.0002% CHS, 0.25 mM domperidone
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 427625
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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