7D92

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P4(3)2(1)2 symmetry)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state.

Kanai, R.Cornelius, F.Ogawa, H.Motoyama, K.Vilsen, B.Toyoshima, C.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2020438118
  • Primary Citation of Related Structures:  
    7D91, 7D92, 7D93, 7D94, 7DDF, 7DDH, 7DDI, 7DDK, 7DDL

  • PubMed Abstract: 

    The sodium pump (Na + , K + -ATPase, NKA) is vital for animal cells, as it actively maintains Na + and K + electrochemical gradients across the cell membrane. It is a target of cardiotonic steroids (CTSs) such as ouabain and digoxin. As CTSs are almost unique strong inhibitors specific to NKA, a wide range of derivatives has been developed for potential therapeutic use. Several crystal structures have been published for NKA-CTS complexes, but they fail to explain the largely different inhibitory properties of the various CTSs. For instance, although CTSs are thought to inhibit ATPase activity by binding to NKA in the E2P state, we do not know if large conformational changes accompany binding, as no crystal structure is available for the E2P state free of CTS. Here, we describe crystal structures of the BeF 3 - complex of NKA representing the E2P ground state and then eight crystal structures of seven CTSs, including rostafuroxin and istaroxime, two new members under clinical trials, in complex with NKA in the E2P state. The conformations of NKA are virtually identical in all complexes with and without CTSs, showing that CTSs bind to a preformed cavity in NKA. By comparing the inhibitory potency of the CTSs measured under four different conditions, we elucidate how different structural features of the CTSs result in different inhibitory properties. The crystal structures also explain K + -antagonism and suggest a route to isoform specific CTSs.


  • Organizational Affiliation

    Institute for Quantitative Biosciences, The University of Tokyo, 113-0032 Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-11,016Sus scrofaMutation(s): 0 
EC: 7.2.2.13
Membrane Entity: Yes 
UniProt
Find proteins for P05024 (Sus scrofa)
Explore P05024 
Go to UniProtKB:  P05024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05024
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1303Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05027 (Sus scrofa)
Explore P05027 
Go to UniProtKB:  P05027
Entity Groups  
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UniProt GroupP05027
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FXYD domain-containing ion transport regulatorC [auth G]65Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58K79
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H0C (Subject of Investigation/LOI)
Query on H0C

Download Ideal Coordinates CCD File 
Q [auth A][(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S},5~{S},8~{R},9~{S},10~{R},11~{R},13~{R},14~{S},17~{R})-10-(hydroxymethyl)-13-methyl-1,5,11,14-tetrakis(oxidanyl)-17-(5-oxidanylidene-2~{H}-furan-3-yl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-6-methyl-3,5-bis(oxidanyl)oxan-4-yl] anthracene-9-carboxylate
C44 H52 O13
CSNRMZGUGASWCS-XLAOFTCCSA-N
PCW
Query on PCW

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CLR
Query on CLR

Download Ideal Coordinates CCD File 
H [auth A],
R [auth B],
T [auth G]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

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S [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.234α = 90
b = 84.234β = 90
c = 646.262γ = 90
Software Package:
Software NamePurpose
BSSdata collection
DENZOdata reduction
SCALEPACKdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16K18500
Japan Society for the Promotion of Science (JSPS)Japan16H02499
Japan Society for the Promotion of Science (JSPS)Japan19H00975
Danish Council for Independent ResearchDenmarkDFF7016-00193B
Danish Council for Independent ResearchDenmarkDFF4183-00011A
Novo Nordisk FoundationDenmarkNNF13OC0013409
Novo Nordisk FoundationDenmarkNNF13OC0006555

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description