5AVX

Kinetics by X-ray crystallography: Tl+-substitution of bound K+ in the E2.MgF42-.2K+ crystal after 20 min


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.315 

wwPDB Validation 3D Report Full Report



Literature

Sequential substitution of K(+) bound to Na(+),K(+)-ATPase visualized by X-ray crystallography.

Ogawa, H.Cornelius, F.Hirata, A.Toyoshima, C.

(2015) Nat Commun 6: 8004-8004

  • DOI: 10.1038/ncomms9004
  • Primary Citation of Related Structures:  
    5AVZ, 5AVS, 5AW4, 5AVR, 5AW3, 5AVU, 5AW6, 5AVT, 5AW5, 5AVW

  • PubMed Abstract: 
  • Na(+),K(+)-ATPase transfers three Na(+) from the cytoplasm into the extracellular medium and two K(+) in the opposite direction per ATP hydrolysed. The binding and release of Na(+) and K(+) are all thought to occur sequentially. Here we demonstrate b ...

    Na(+),K(+)-ATPase transfers three Na(+) from the cytoplasm into the extracellular medium and two K(+) in the opposite direction per ATP hydrolysed. The binding and release of Na(+) and K(+) are all thought to occur sequentially. Here we demonstrate by X-ray crystallography of the ATPase in E2·MgF4(2-)·2K(+), a state analogous to E2·Pi·2K(+), combined with isotopic measurements, that the substitution of the two K(+) with congeners in the extracellular medium indeed occurs at different rates, substantially faster at site II. An analysis of thermal movements of protein atoms in the crystal shows that the M3-M4E helix pair opens and closes the ion pathway leading to the extracellular medium, allowing K(+) at site II to be substituted first. Taken together, these results indicate that site I K(+) is the first cation to bind to the empty cation-binding sites after releasing three Na(+).


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na, K-ATPase alpha subunitA1028Squalus acanthiasMutation(s): 0 
Gene Names: atn1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase, E2.MgF42-, Tl+ substitution at 0.75 min
Find proteins for Q4H132 (Squalus acanthias)
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Go to UniProtKB:  Q4H132
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Na+,K+-ATPase beta subunitB305Squalus acanthiasMutation(s): 0 
Gene Names: atp1b1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase, E2.MgF42-, Tl+ substitution at 0.75 min
Find proteins for C4IX13 (Squalus acanthias)
Explore C4IX13 
Go to UniProtKB:  C4IX13
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholemman-like proteinG74Squalus acanthiasMutation(s): 0 
Gene Names: fxyd10
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase, E2.MgF42-, Tl+ substitution at 0.75 min
Find proteins for Q70Q12 (Squalus acanthias)
Explore Q70Q12 
Go to UniProtKB:  Q70Q12
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download CCD File 
B
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
NAG
Query on NAG

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B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TL
Query on TL

Download CCD File 
A
THALLIUM (I) ION
Tl
ZLUSCZLCHQSJRU-UHFFFAOYSA-N
 Ligand Interaction
MF4
Query on MF4

Download CCD File 
A
TETRAFLUOROMAGNESATE(2-)
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
 Ligand Interaction
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.315 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.053α = 90
b = 50.768β = 103.67
c = 163.397γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology of JapanJapan--
The Danish Medical Research FoundationDenmark--
The Danish Agency for Science Technology and InnovationDenmark--
The Novo Nordisk FoundationDenmark--

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary