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- EMDB-80904: D-pantothenic acid-bound SMVT in the occluded state -

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Basic information

Entry
Database: EMDB / ID: EMD-80904
TitleD-pantothenic acid-bound SMVT in the occluded state
Map data
Sample
  • Complex: SMVT in complex with D-pantothenic acid in an occluded conformation
    • Protein or peptide: Sodium-dependent multivitamin transporter
  • Ligand: PANTOTHENOIC ACID
KeywordsSodium-dependent multivitamin transporter / SMVT / SLC5A6 / D-pantothenic acid / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium-dependent multivitamin transmembrane transporter activity / pantothenate transmembrane transporter activity / pantothenate:sodium symporter activity / pantothenate transmembrane transport / biotin import across plasma membrane / Transport of vitamins, nucleosides, and related molecules / vitamin transmembrane transporter activity / iodide transmembrane transport / biotin metabolic process / biotin transmembrane transporter activity ...sodium-dependent multivitamin transmembrane transporter activity / pantothenate transmembrane transporter activity / pantothenate:sodium symporter activity / pantothenate transmembrane transport / biotin import across plasma membrane / Transport of vitamins, nucleosides, and related molecules / vitamin transmembrane transporter activity / iodide transmembrane transport / biotin metabolic process / biotin transmembrane transporter activity / biotin transport / iodide transmembrane transporter activity / Vitamin B5 (pantothenate) metabolism / Biotin transport and metabolism / sodium ion transport / transport across blood-brain barrier / basal plasma membrane / brush border membrane / basolateral plasma membrane / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
: / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
Sodium-dependent multivitamin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang Z / Zhen Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471252 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for multivitamin recognition and transport by human SMVT.
Authors: Qiuxin Zhen / Mingshuai Wang / Zhe Zhang /
Abstract: The human sodium-dependent multivitamin transporter (SMVT, SLC5A6) mediates cellular uptake of essential metabolic cofactors, including biotin, pantothenate, and lipoate. Its dysfunction is ...The human sodium-dependent multivitamin transporter (SMVT, SLC5A6) mediates cellular uptake of essential metabolic cofactors, including biotin, pantothenate, and lipoate. Its dysfunction is associated with neurological disorders, metabolic abnormalities, and cancer. However, the molecular mechanism underlying its multi-substrate transport has remained elusive. Here, we present cryo-electron microscopy structures of human SMVT in three conformational states: occluded, outward-open, and inward-open. These structural snapshots capture the complete transport cycle and reveal a conserved substrate-binding pocket near a kinked transmembrane helix (TM1). Within this pocket, substrate carboxyl groups are electrostatically anchored, while distinct chemical moieties interact with specific polar and hydrophobic residues. Functional assays identify key binding residues and elucidate the pathogenic effects of disease-associated mutations. Further structural analysis delineates the principles of substrate discrimination within the SLC5 transporter family. Together, our work provides a structural framework for SMVT's polyspecificity and lays a foundation for understanding related diseases and developing targeted therapeutic strategies.
History
DepositionMay 16, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80904.png

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 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: 0.1
Minimum - Maximum-0.8806951 - 0.9753812
Average (Standard dev.)0.0007061031 (±0.021535141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80904_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80904_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 : SMVT in complex with D-pantothenic acid in an occluded conformation

EntireName: SMVT in complex with D-pantothenic acid in an occluded conformation
Components
  • Complex: SMVT in complex with D-pantothenic acid in an occluded conformation
    • Protein or peptide: Sodium-dependent multivitamin transporter
  • Ligand: PANTOTHENOIC ACID

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Supramolecule #1: SMVT in complex with D-pantothenic acid in an occluded conformation

SupramoleculeName: SMVT in complex with D-pantothenic acid in an occluded conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70 KDa

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Macromolecule #1: Sodium-dependent multivitamin transporter

MacromoleculeName: Sodium-dependent multivitamin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.000703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVGVSTSAP LSPTSGTSVG MSTFSIMDYV VFVLLLVLSL AIGLYHACRG WGRHTVGELL MADRKMGCLP VALSLLATFQ SAVAILGVP SEIYRFGTQY WFLGCCYFLG LLIPAHIFIP VFYRLHLTSA YEYLELRFNK TVRVCGTVTF IFQMVIYMGV V LYAPSLAL ...String:
MSVGVSTSAP LSPTSGTSVG MSTFSIMDYV VFVLLLVLSL AIGLYHACRG WGRHTVGELL MADRKMGCLP VALSLLATFQ SAVAILGVP SEIYRFGTQY WFLGCCYFLG LLIPAHIFIP VFYRLHLTSA YEYLELRFNK TVRVCGTVTF IFQMVIYMGV V LYAPSLAL NAVTGFDLWL SVLALGIVCT VYTALGGLKA VIWTDVFQTL VMFLGQLAVI IVGSAKVGGL GRVWAVASQH GR ISGFELD PDPFVRHTFW TLAFGGVFMM LSLYGVNQAQ VQRYLSSRTE KAAVLSCYAV FPFQQVSLCV GCLIGLVMFA YYQ EYPMSI QQAQAAPDQF VLYFVMDLLK GLPGLPGLFI ACLFSGSLST ISSAFNSLAT VTMEDLIRPW FPEFSEARAI MLSR GLAFG YGLLCLGMAY ISSQMGPVLQ AAISIFGMVG GPLLGLFCLG MFFPCANPPG AVVGLLAGLV MAFWIGIGSI VTSMG SSMS RLEEELRRRL TETGLQRFYS LSYLWYSAHN STTVIVVGLI VSLLTGRMRG RSLNPATIYP VLPKLLSLLP LSCQKR LHC RSYGQDHLDT GLFPEKPRNG VLGDSRDKEA MALDGTAYQG SSSTCILQET SLSNSLEVLF Q

UniProtKB: Sodium-dependent multivitamin transporter, Sodium-dependent multivitamin transporter

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Macromolecule #2: PANTOTHENOIC ACID

MacromoleculeName: PANTOTHENOIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: PAU
Molecular weightTheoretical: 219.235 Da
Chemical component information

ChemComp-PAU:
PANTOTHENOIC ACID

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 259504
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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