4HYT | pdb_00004hyt

Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.244 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Crystal structure of the high-affinity Na+,K+-ATPase-ouabain complex with Mg2+ bound in the cation binding site.

Laursen, M.Yatime, L.Nissen, P.Fedosova, N.U.

(2013) Proc Natl Acad Sci U S A 110: 10958-10963

  • DOI: https://doi.org/10.1073/pnas.1222308110
  • Primary Citation Related Structures: 
    4HYT

  • PubMed Abstract: 

    The Na(+),K(+)-ATPase maintains electrochemical gradients for Na(+) and K(+) that are critical for animal cells. Cardiotonic steroids (CTSs), widely used in the clinic and recently assigned a role as endogenous regulators of intracellular processes, are highly specific inhibitors of the Na(+),K(+)-ATPase. Here we describe a crystal structure of the phosphorylated pig kidney Na(+),K(+)-ATPase in complex with the CTS representative ouabain, extending to 3.4 Å resolution. The structure provides key details on CTS binding, revealing an extensive hydrogen bonding network formed by the β-surface of the steroid core of ouabain and the side chains of αM1, αM2, and αM6. Furthermore, the structure reveals that cation transport site II is occupied by Mg(2+), and crystallographic studies indicate that Rb(+) and Mn(2+), but not Na(+), bind to this site. Comparison with the low-affinity [K2]E2-MgF(x)-ouabain structure [Ogawa et al. (2009) Proc Natl Acad Sci USA 106(33):13742-13747) shows that the CTS binding pocket of [Mg]E2P allows deep ouabain binding with possible long-range interactions between its polarized five-membered lactone ring and the Mg(2+). K(+) binding at the same site unwinds a turn of αM4, dragging residues Ile318-Val325 toward the cation site and thereby hindering deep ouabain binding. Thus, the structural data establish a basis for the interpretation of the biochemical evidence pointing at direct K(+)-Mg(2+) competition and explain the well-known antagonistic effect of K(+) on CTS binding.


  • Organizational Affiliation
    • Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, DK-8000 Aarhus C, Denmark.

Macromolecule Content 

  • Total Structure Weight: 320.76 kDa 
  • Atom Count: 21,220 
  • Modeled Residue Count: 2,632 
  • Deposited Residue Count: 2,778 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-1A,
D [auth C]
1,021Sus scrofaMutation(s): 0 
EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1B,
E [auth D]
303Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05027 (Sus scrofa)
Explore P05027 
Go to UniProtKB:  P05027
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05027
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Na+/K+ ATPase gamma subunit transcript variant aC [auth G],
F [auth E]
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 GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth F]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
17F

Query on 17F



Download:Ideal Coordinates CCD File
EA [auth D],
O [auth A],
P [auth A],
T [auth B],
V [auth G]
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
C42 H78 N O10 P
WTBFLCSPLLEDEM-JIDRGYQWSA-N
OBN

Query on OBN



Download:Ideal Coordinates CCD File
K [auth A],
Z [auth C]
OUABAIN
C29 H44 O12
LPMXVESGRSUGHW-HBYQJFLCSA-N
CE1

Query on CE1



Download:Ideal Coordinates CCD File
GA [auth E],
Q [auth A]
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
1DS

Query on 1DS



Download:Ideal Coordinates CCD File
N [auth A]1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside
C22 H40 O12
DSDLUVQAJPJFTK-AJFJJNJGSA-N
1AT

Query on 1AT



Download:Ideal Coordinates CCD File
M [auth A]beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside
C22 H40 O12
STVGXWVWPOLILC-LUQRLMJOSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
AA [auth C],
FA [auth E],
L [auth A],
U [auth G]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
BA [auth D],
CA [auth D],
DA [auth D],
R [auth B],
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
H [auth A]
I [auth A]
J [auth A]
W [auth C]
X [auth C]
H [auth A],
I [auth A],
J [auth A],
W [auth C],
X [auth C],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PHD
Query on PHD
A,
D [auth C]
L-PEPTIDE LINKINGC4 H8 N O7 PASP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.244 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.47α = 90
b = 118.08β = 90
c = 494.66γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
RemDAqdata collection
XDSdata reduction
diffractiondata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary