26VD | pdb_000026vd

SMVT in the outward-open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 26VD

This is version 1.0 of the entry. See complete history

Literature

Structural basis for multivitamin recognition and transport by human SMVT.

Zhen, Q.Wang, M.Zhang, Z.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-74948-3
  • Primary Citation Related Structures: 
    26VA, 26VB, 26VC, 26VD, 26VE

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 68 kDa 
  • Atom Count: 3,906 
  • Modeled Residue Count: 508 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium-dependent multivitamin transporter624Homo sapiensMutation(s): 0 
Gene Names: SLC5A6SMVT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y289 (Homo sapiens)
Explore Q9Y289 
Go to UniProtKB:  Q9Y289
PHAROS:  Q9Y289
GTEx:  ENSG00000138074 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y289
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32471252

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release