8W6G | pdb_00008w6g

NaDC1 with inhibitor ACA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8W6G

This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.

Chi, X.Chen, Y.Li, Y.Dai, L.Zhang, Y.Shen, Y.Chen, Y.Shi, T.Yang, H.Wang, Z.Yan, R.

(2024) Sci Adv 10: eadl3685-eadl3685

  • DOI: https://doi.org/10.1126/sciadv.adl3685
  • Primary Citation Related Structures: 
    8W6C, 8W6D, 8W6G, 8W6H, 8W6N, 8W6O, 8W6T

  • PubMed Abstract: 

    The solute carrier 13 (SLC13) family comprises electrogenic sodium ion-coupled anion cotransporters, segregating into sodium ion-sulfate cotransporters (NaSs) and sodium ion-di- and-tricarboxylate cotransporters (NaDCs). NaS1 and NaDC1 regulate sulfate homeostasis and oxidative metabolism, respectively. NaS1 deficiency affects murine growth and fertility, while NaDC1 affects urinary citrate and calcium nephrolithiasis. Despite their importance, the mechanisms of substrate recognition and transport remain insufficiently characterized. In this study, we determined the cryo-electron microscopy structures of human NaS1, capturing inward-facing and combined inward-facing/outward-facing conformations within a dimer both in apo and sulfate-bound states. In addition, we elucidated NaDC1's outward-facing conformation, encompassing apo, citrate-bound, and N -( p -amylcinnamoyl) anthranilic acid (ACA) inhibitor-bound states. Structural scrutiny illuminates a detailed elevator mechanism driving conformational changes. Notably, the ACA inhibitor unexpectedly binds primarily anchored by transmembrane 2 (TM2), Loop 10, TM11, and TM6a proximate to the cytosolic membrane. Our findings provide crucial insights into SLC13 transport mechanisms, paving the way for future drug design.


  • Organizational Affiliation
    • State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Science, Xiamen University, Xiamen 361102, Fujian Province, China.

Macromolecule Content 

  • Total Structure Weight: 134.93 kDa 
  • Atom Count: 8,314 
  • Modeled Residue Count: 1,054 
  • Deposited Residue Count: 1,210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 13 member 2
A, B
605Homo sapiensMutation(s): 1 
Gene Names: SLC13A2NADC1SDCT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13183 (Homo sapiens)
Explore Q13183 
Go to UniProtKB:  Q13183
PHAROS:  Q13183
GTEx:  ENSG00000007216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13183
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PH
(Subject of Investigation/LOI)

Query on 3PH



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
Y01

Query on Y01



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
VIJ

Query on VIJ



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
2-[[(~{E})-3-(4-pentylphenyl)prop-2-enoyl]amino]benzoic acid
C21 H23 N O3
GAMRBCZMOOMBSQ-CCEZHUSRSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32100975

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release