8ZYJ | pdb_00008zyj

Cryo-EM structure of human testis-specific Na+,K+-ATPase alpha4 in ouabain-bound form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Molecular Structure of the Na + ,K + -ATPase alpha 4 beta 1 Isoform in Its Ouabain-Bound Conformation.

Abe, K.McDermott, J.Valia Madapally, H.Marimuthu, P.Gopalasingam, C.C.Gerle, C.Shigematsu, H.Khandelia, H.Blanco, G.

(2024) Int J Mol Sci 25

  • DOI: https://doi.org/10.3390/ijms252212397
  • Primary Citation of Related Structures:  
    8ZYJ

  • PubMed Abstract: 

    Na + ,K + -ATPase is the active ion transport system that maintains the electrochemical gradients for Na + and K + across the plasma membrane of most animal cells. Na + ,K + -ATPase is constituted by the association of two major subunits, a catalytic α and a glycosylated β subunit, both of which exist as different isoforms (in mammals known as α1, α2, α3, α4, β1, β2 and β3). Na + ,K + -ATPase α and β isoforms assemble in different combinations to produce various isozymes with tissue specific expression and distinct biochemical properties. Na + ,K + -ATPase α4β1 is only found in male germ cells of the testis and is mainly expressed in the sperm flagellum, where it plays a critical role in sperm motility and male fertility. Here, we report the molecular structure of Na + ,K + -ATPase α4β1 at 2.37 Å resolution in the ouabain-bound state and in the presence of beryllium fluoride. Overall, Na + ,K + -ATPase α4 structure exhibits the basic major domains of a P-Type ATPase, resembling Na + ,K + -ATPase α1, but has differences specific to its distinct sequence. Dissimilarities include the site where the inhibitor ouabain binds. Molecular simulations indicate that glycosphingolipids can bind to a putative glycosphingolipid binding site, which could potentially modulate Na + ,K + -ATPase α4 activity. This is the first experimental evidence for the structure of Na + ,K + -ATPase α4β1. These data provide a template that will aid in better understanding the function Na + ,K + -ATPase α4β1 and will be important for the design and development of compounds that can modulate Na + ,K + -ATPase α4 activity for the purpose of improving male fertility or to achieve male contraception.


  • Organizational Affiliation
    • Department of Chemistry, Faculty of Science, Hokkaido University, Hokkaido 060-0808, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-4984Homo sapiensMutation(s): 0 
Gene Names: ATP1A4ATP1AL2
EC: 7.2.2.13
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13733 (Homo sapiens)
Explore Q13733 
Go to UniProtKB:  Q13733
PHAROS:  Q13733
GTEx:  ENSG00000132681 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13733
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1303Homo sapiensMutation(s): 0 
Gene Names: ATP1B1ATP1B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05026 (Homo sapiens)
Explore P05026 
Go to UniProtKB:  P05026
PHAROS:  P05026
GTEx:  ENSG00000143153 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05026
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q7G (Subject of Investigation/LOI)
Query on Q7G

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
J [auth B]
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
C56 H92 O25
LKBFXDNKNZXHHW-NXLTVWPKSA-N
PCW
Query on PCW

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H [auth A]1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
OBN (Subject of Investigation/LOI)
Query on OBN

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F [auth A]OUABAIN
C29 H44 O12
LPMXVESGRSUGHW-HBYQJFLCSA-N
CLR
Query on CLR

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E [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

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

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C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-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: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan24K01975

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Data collection, Database references