7S1X | pdb_00007s1x

Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide

• PDB DOI: https://doi.org/10.2210/pdb7S1X/pdb
• EM Map EMD-24807: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Mammalian expression vector BsrGI-MCS-pcDNA3.1
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2021-09-02 Released: 2022-05-25 
• Deposition Author(s): Zhao, Y.X., Cao, E.H.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide

Zhao, Y., Roy, K., Vidossich, P., Cancedda, L., De Vivo, M., Forbush, B., Cao, E.

(2022) Nat Commun 13: 2747

• DOI: https://doi.org/10.1038/s41467-022-30407-3

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 264.66 kDa 
• Atom Count: 12,658 
• Modeled Residue Count: 1,742 
• Deposited Residue Count: 2,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 12 member 2	A [auth B], B [auth A]	1,216	Homo sapiens	Mutation(s): 3  Gene Names: SLC12A2, NKCC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P55011 (Homo sapiens) Explore P55011  Go to UniProtKB:  P55011
PHAROS:  P55011 GTEx:  ENSG00000064651

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
82U (Subject of Investigation/LOI)	C [auth B], F [auth A]	3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid C17 H20 N2 O5 S MAEIEVLCKWDQJH-UHFFFAOYSA-N
K	D [auth B], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	E [auth B], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
82U	BindingDB:  7S1X	IC50: 1540 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Zhao, Y.X., Cao, E.H.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary
• Version 1.2: 2025-05-28
  Changes: Data collection