8FHO | pdb_00008fho

Cryo-EM structure of human NCC (class 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8FHO

This is version 1.4 of the entry. See complete history

Literature

Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter.

Fan, M.Zhang, J.Lee, C.L.Zhang, J.Feng, L.

(2023) Nature 614: 788-793

  • DOI: https://doi.org/10.1038/s41586-023-05718-0
  • Primary Citation Related Structures: 
    8FHN, 8FHO, 8FHP, 8FHQ, 8FHR, 8FHT

  • PubMed Abstract: 

    The sodium-chloride cotransporter (NCC) is critical for kidney physiology 1 . The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron 2,3 , and mutations in the NCC cause the salt-wasting disease Gitelman syndrome 4 . As a key player in salt handling, the NCC regulates blood pressure and is the target of thiazide diuretics, which have been widely prescribed as first-line medications to treat hypertension for more than 60 years 5-7 . Here we determined the structures of human NCC alone and in complex with a commonly used thiazide diuretic using cryo-electron microscopy. These structures, together with functional studies, reveal major conformational states of the NCC and an intriguing regulatory mechanism. They also illuminate how thiazide diuretics specifically interact with the NCC and inhibit its transport function. Our results provide critical insights for understanding the Na-Cl cotransport mechanism of the NCC, and they establish a framework for future drug design and for interpreting disease-related mutations.


  • Organizational Affiliation
    • Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 363.06 kDa 
  • Atom Count: 13,624 
  • Modeled Residue Count: 1,723 
  • Deposited Residue Count: 3,276 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 12 member 2,Solute carrier family 12 member 3 chimera
A, B, C
1,092Danio rerioHomo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: slc12a2nkcc1SLC12A3NCCTSC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P55017 (Homo sapiens)
Explore P55017 
Go to UniProtKB:  P55017
PHAROS:  P55017
GTEx:  ENSG00000070915 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55017
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on ATP



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
XZF
(Subject of Investigation/LOI)

Query on XZF



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
Polythiazide
C11 H13 Cl F3 N3 O4 S3
CYLWJCABXYDINA-JTQLQIEISA-N
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-03-08
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-06-04
    Changes: Data collection