7ZGO | pdb_00007zgo

Cryo-EM structure of human NKCC1 (TM domain)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZGO

This is version 1.3 of the entry. See complete history

Literature

Cryo-EM structure of the human NKCC1 transporter reveals mechanisms of ion coupling and specificity.

Neumann, C.Rosenbaek, L.L.Flygaard, R.K.Habeck, M.Karlsen, J.L.Wang, Y.Lindorff-Larsen, K.Gad, H.H.Hartmann, R.Lyons, J.A.Fenton, R.A.Nissen, P.

(2022) EMBO J 41: e110169-e110169

  • DOI: https://doi.org/10.15252/embj.2021110169
  • Primary Citation Related Structures: 
    7ZGO

  • PubMed Abstract: 

    The sodium-potassium-chloride transporter NKCC1 of the SLC12 family performs Na + -dependent Cl - - and K + -ion uptake across plasma membranes. NKCC1 is important for regulating cell volume, hearing, blood pressure, and regulation of hyperpolarizing GABAergic and glycinergic signaling in the central nervous system. Here, we present a 2.6 Å resolution cryo-electron microscopy structure of human NKCC1 in the substrate-loaded (Na + , K + , and 2 Cl - ) and occluded, inward-facing state that has also been observed for the SLC6-type transporters MhsT and LeuT. Cl - binding at the Cl1 site together with the nearby K + ion provides a crucial bridge between the LeuT-fold scaffold and bundle domains. Cl - -ion binding at the Cl2 site seems to undertake a structural role similar to conserved glutamate of SLC6 transporters and may allow for Cl - -sensitive regulation of transport. Supported by functional studies in mammalian cells and computational simulations, we describe a putative Na + release pathway along transmembrane helix 5 coupled to the Cl2 site. The results provide insight into the structure-function relationship of NKCC1 with broader implications for other SLC12 family members.


  • Organizational Affiliation
    • Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus, Denmark.

Macromolecule Content 

  • Total Structure Weight: 272.15 kDa 
  • Atom Count: 7,754 
  • Modeled Residue Count: 940 
  • Deposited Residue Count: 2,432 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 12 member 2
A, B
1,216Homo sapiensMutation(s): 0 
Gene Names: SLC12A2NKCC1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55011
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
(Subject of Investigation/LOI)

Query on POV



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
R [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
R [auth B],
S [auth B],
T [auth B]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
Y01
(Subject of Investigation/LOI)

Query on Y01



Download:Ideal Coordinates CCD File
K [auth A]
L [auth A]
M [auth A]
U [auth B]
V [auth B]
K [auth A],
L [auth A],
M [auth A],
U [auth B],
V [auth B],
W [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
K
(Subject of Investigation/LOI)

Query on K



Download:Ideal Coordinates CCD File
D [auth A],
O [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
P [auth B],
Q [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
(Subject of Investigation/LOI)

Query on NA



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmark2015-3225
LundbeckfondenDenmarkR310-2018-3713
Leducq FoundationFrance17CVD05
Novo Nordisk FoundationDenmarkNNF21OC0067647
Novo Nordisk FoundationDenmarkNNF17OC0029724
Novo Nordisk FoundationDenmarkNNF19OC0058439

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references, Refinement description
  • Version 1.2: 2024-09-25
    Changes: Data collection, Refinement description, Source and taxonomy
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary