8JFZ | pdb_00008jfz

Cryo-EM structure of Na+,K+-ATPase in the E1.Mg2+ state.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8JFZ

This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Na + ,K + -ATPase reveal the mechanism that converts the K + -bound form to Na + -bound form and opens and closes the cytoplasmic gate.

Kanai, R.Vilsen, B.Cornelius, F.Toyoshima, C.

(2023) FEBS Lett 597: 1957-1976

  • DOI: https://doi.org/10.1002/1873-3468.14689
  • Primary Citation Related Structures: 
    8JBK, 8JBL, 8JBM, 8JFZ

  • PubMed Abstract: 

    Na + ,K + -ATPase (NKA) plays a pivotal role in establishing electrochemical gradients for Na + and K + across the cell membrane by alternating between the E1 (showing high affinity for Na + and low affinity for K + ) and E2 (low affinity to Na + and high affinity to K + ) forms. Presented here are two crystal structures of NKA in E1·Mg 2+ and E1·3Na + states at 2.9 and 2.8 Å resolution, respectively. These two E1 structures fill a gap in our description of the NKA reaction cycle based on the atomic structures. We describe how NKA converts the K + -bound E2·2K + form to an E1 (E1·Mg 2+ ) form, which allows high-affinity Na + binding, eventually closing the cytoplasmic gate (in E1 ~ P·ADP·3Na + ) after binding three Na + , while keeping the extracellular ion pathway sealed. We now understand previously unknown functional roles for several parts of NKA and that NKA uses even the lipid bilayer for gating the ion pathway.


  • Organizational Affiliation
    • Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Japan.

Macromolecule Content 

  • Total Structure Weight: 343.28 kDa 
  • Atom Count: 22,340 
  • Modeled Residue Count: 2,642 
  • Deposited Residue Count: 2,854 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na+,K+-ATPase beta subunitA [auth D],
D [auth B]
305Squalus acanthiasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C4IX13 (Squalus acanthias)
Explore C4IX13 
Go to UniProtKB:  C4IX13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4IX13
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Na, K-ATPase alpha subunitB [auth C],
E [auth A]
1,028Squalus acanthiasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q4H132 (Squalus acanthias)
Explore Q4H132 
Go to UniProtKB:  Q4H132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4H132
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FXYD domain-containing ion transport regulatorC [auth E],
F [auth G]
94Squalus acanthiasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q70Q12 (Squalus acanthias)
Explore Q70Q12 
Go to UniProtKB:  Q70Q12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70Q12
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth F],
K
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G82348BZ
GlyCosmos: G82348BZ
GlyGen: G82348BZ
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, L
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G61751GZ
GlyCosmos: G61751GZ
GlyGen: G61751GZ
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I, M
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G42466VF
GlyCosmos: G42466VF
GlyGen: G42466VF
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW

Query on PCW



Download:Ideal Coordinates CCD File
CA [auth E]
HA [auth A]
IA [auth A]
JA [auth A]
KA [auth A]
CA [auth E],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
TA [auth G],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CLR

Query on CLR



Download:Ideal Coordinates CCD File
BA [auth E]
DA [auth B]
EA [auth A]
FA [auth A]
GA [auth A]
BA [auth E],
DA [auth B],
EA [auth A],
FA [auth A],
GA [auth A],
O [auth D],
P [auth C],
SA [auth G]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AA [auth C],
QA [auth A],
RA [auth A],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.3
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP19H00975
Japan Society for the Promotion of Science (JSPS)JapanJP21K06109

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary