9QJ2 | pdb_00009qj2

Titin kinase (isoform b) from medaka


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Molecular identifiers of the evolutionarily conserved titin pseudokinase.

Dorendorf, T.Gravenhorst, P.Mayans, O.

(2026) Biochem J 483: 55-70

  • DOI: https://doi.org/10.1042/BCJ20253442
  • Primary Citation of Related Structures:  
    9QJ2

  • PubMed Abstract: 

    Titin kinase (TK) is an enigmatic pseudokinase specific to the striated muscle of vertebrates. Embedded within the contractile sarcomere and flanked by extensible regulatory tails, TK is thought to act as a mechanoreceptor that senses mechanical signals arising from muscle function. Studies on TK so far have focused narrowly on the human representative, whose phosphotransfer activity remains questioned. To investigate whether the pseudokinase character is a hallmark of TK, we studied sequences of distantly evolved fish representatives and rationalized conservation patterns by solving the crystal structure of TK from medaka (isoform b). We find that sequence deviations in functional motifs involved in ATP and magnesium binding, respectively θxK (θ: bulky hydrophobic residue) and EFG, are evolutionarily conserved in TK. Beyond the kinase domain, N- and C-terminal flanking tails show remarkable structural similarity across orthologues, even though sequence conservation is limited to individual residues and short motifs: a YD-motif in the N-terminal tail; a [R/K]H[R/K]RYY sequence, a R-7x-R motif and position -2 of the latter in the C-terminal tail. Motifs in the C-terminal tail consistently covary with the divergent functional motifs of TK, being part of its pseudokinase signature. Contrary with these general features, the putatively inhibitory interaction of the catalytic aspartate with a tyrosine from loop P+1 is primarily confined to mammals. Finally, based on sequence clustering analysis, we identify TK subgroupings and propose a classification of titin genes from fish into a and b isoforms (ttna and ttnb) that can assist future studies. A curated genomic annotation is provided.


  • Organizational Affiliation
    • Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78457, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chains: A,B
A, B
354Oryzias latipesMutation(s): 0 
UniProt
Find proteins for A0A3P9GXN4 (Oryzias latipes)
Explore A0A3P9GXN4 
Go to UniProtKB:  A0A3P9GXN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3P9GXN4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.735α = 90
b = 56.08β = 104.284
c = 120.245γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references