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 OPM PDBTM mpstruc

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

wwPDB Validation 3D Report Full Report

Validation slider image for 7S1X

This is version 1.2 of the entry. See complete history.

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55011
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
82U (Subject of Investigation/LOI) Query on 82U Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain F [auth A] MOL2 format, chain C [auth B] MOL2 format, chain F [auth A] mmCIF format, chain C [auth B] mmCIF format, chain F [auth A]	C [auth B], F [auth A]	3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid C₁₇ H₂₀ N₂ O₅ S MAEIEVLCKWDQJH-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain G [auth A] MOL2 format, chain D [auth B] MOL2 format, chain G [auth A] mmCIF format, chain D [auth B] mmCIF format, chain G [auth A]	D [auth B], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain G [auth A] Interactions & Density Focus chain D [auth B] Focus chain G [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain H [auth A] MOL2 format, chain E [auth B] MOL2 format, chain H [auth A] mmCIF format, chain E [auth B] mmCIF format, chain H [auth A]	E [auth B], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain H [auth A] Interactions & Density Focus chain E [auth B] Focus chain H [auth A]

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.