6NPH | pdb_00006nph

Structure of NKCC1 TM domain

• PDB DOI: https://doi.org/10.2210/pdb6NPH/pdb
• EM Map EMD-0470: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Danio rerio
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2019-01-17 Released: 2019-07-31 
• Deposition Author(s): Feng, L., Liao, M.F., Orlando, B., Zhang, J.R.

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Experimental Data Snapshot

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

Literature

Structure and mechanism of the cation-chloride cotransporter NKCC1.

Chew, T.A., Orlando, B.J., Zhang, J., Latorraca, N.R., Wang, A., Hollingsworth, S.A., Chen, D.H., Dror, R.O., Liao, M., Feng, L.

(2019) Nature 572: 488-492

• PubMed: 31367042 
• DOI: https://doi.org/10.1038/s41586-019-1438-2
• Primary Citation Related Structures: 
  6NPH, 6NPJ, 6NPK, 6NPL


• PubMed Abstract: 
  

  Cation-chloride cotransporters (CCCs) mediate the electroneutral transport of chloride, potassium and/or sodium across the membrane. They have critical roles in regulating cell volume, controlling ion absorption and secretion across epithelia, and maintaining intracellular chloride homeostasis. These transporters are primary targets for some of the most commonly prescribed drugs. Here we determined the cryo-electron microscopy structure of the Na-K-Cl cotransporter NKCC1, an extensively studied member of the CCC family, from Danio rerio. The structure defines the architecture of this protein family and reveals how cytosolic and transmembrane domains are strategically positioned for communication. Structural analyses, functional characterizations and computational studies reveal the ion-translocation pathway, ion-binding sites and key residues for transport activity. These results provide insights into ion selectivity, coupling and translocation, and establish a framework for understanding the physiological functions of CCCs and interpreting disease-related mutations.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Merck & Co., South San Francisco, CA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Biophysics Program, Stanford University, Stanford, CA, USA. [e-mail].
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 106.78 kDa 
• Atom Count: 7,504 
• Modeled Residue Count: 944 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 12 (sodium/potassium/chloride transporter), member 2	A, B	472	Danio rerio	Mutation(s): 0  Gene Names: slc12a2 Membrane Entity: Yes
UniProt
Find proteins for A0A0G2KTI4 (Danio rerio) Explore A0A0G2KTI4  Go to UniProtKB:  A0A0G2KTI4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C42 H82 N O8 P WTJKGGKOPKCXLL-PFDVCBLKSA-N
K	F [auth A], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	G [auth A], H [auth A], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Feng, L., Liao, M.F., Orlando, B., Zhang, J.R.

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2019-08-28
  Changes: Data collection, Database references
• Version 1.3: 2020-01-29
  Changes: Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary