7Y46 | pdb_00007y46

Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after addition of ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y46

This is version 1.2 of the entry. See complete history

Literature

Cryo-electron microscopy of Na + ,K + -ATPase reveals how the extracellular gate locks in the E2·2K + state.

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

(2022) FEBS Lett 596: 2513-2524

  • DOI: https://doi.org/10.1002/1873-3468.14437
  • Primary Citation Related Structures: 
    7Y45, 7Y46

  • PubMed Abstract: 

    Na + ,K + -ATPase (NKA) is one of the most important members of the P-type ion-translocating ATPases and plays a pivotal role in establishing electrochemical gradients for Na + and K + across the cell membrane. Presented here is a 3.3 Å resolution structure of NKA in the E2·2K + state solved by cryo-electron microscopy. It is a stable state with two occluded K + after transferring three Na + into the extracellular medium and releasing inorganic phosphate bound to the cytoplasmic P domain. We describe how the extracellular ion pathway wide open in the E2P state becomes closed and locked in E2·2K + , linked to events at the phosphorylation site more than 50 Å away. We also show, although at low resolution, how ATP binding to NKA in E2·2K + relaxes the gating machinery and thereby accelerates the transition into the next step, that is, the release of K + into the cytoplasm, more than 100 times.


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

Macromolecule Content 

  • Total Structure Weight: 330.26 kDa 
  • Atom Count: 21,594 
  • Modeled Residue Count: 2,654 
  • 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 alpha subunitA [auth C],
D [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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Na+,K+-ATPase beta subunitB [auth D],
E [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
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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
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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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW

Query on PCW



Download:Ideal Coordinates CCD File
DA [auth A],
U [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
O [auth C],
X [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
BA [auth A]
CA [auth A]
EA [auth A]
FA [auth B]
S [auth C]
BA [auth A],
CA [auth A],
EA [auth A],
FA [auth B],
S [auth C],
T [auth C],
V [auth C],
W [auth D]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
K

Query on K



Download:Ideal Coordinates CCD File
AA [auth A]
P [auth C]
Q [auth C]
R [auth C]
Y [auth A]
AA [auth A],
P [auth C],
Q [auth C],
R [auth C],
Y [auth A],
Z [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 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)Japan19H00975
Japan Society for the Promotion of Science (JSPS)Japan18K06148
Danish Council for Independent ResearchDenmarkDFF7016-00193B
Danish Council for Independent ResearchDenmarkDFF4183-00011A
Novo Nordisk FoundationDenmarkNNF14OC0013409
Novo Nordisk FoundationDenmarkNNF13OC0006555

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary