7XRB | pdb_00007xrb

human STK19 dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.194 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

STK19 is a DNA/RNA-binding protein critical for DNA damage repair and cell proliferation.

Li, Y.Gong, Y.Zhou, Y.Xiao, Y.Huang, W.Zhou, Q.Tu, Y.Zhao, Y.Zhang, S.Dai, L.Sun, Q.

(2024) J Cell Biol 223

  • DOI: https://doi.org/10.1083/jcb.202301090
  • Primary Citation of Related Structures:  
    7XRB

  • PubMed Abstract: 

    STK19 was originally identified as a manganese-dependent serine/threonine-specific protein kinase, but its function has been highly debated. Here, the crystal structure of STK19 revealed that it does not contain a kinase domain, but three intimately packed winged helix (WH) domains. The third WH domain mediated homodimerization and double-stranded DNA binding, both being important for its nuclear localization. STK19 participated in the nucleotide excision repair (NER) and mismatch repair (MMR) pathways by recruiting damage repair factors such as RPA2 and PCNA. STK19 also bound double-stranded RNA through the DNA-binding interface and regulated the expression levels of many mRNAs. Furthermore, STK19 knockdown cells exhibited very slow cell proliferation, which cannot be rescued by dimerization or DNA-binding mutants. Therefore, this work concludes that STK19 is highly unlikely to be a kinase but a DNA/RNA-binding protein critical for DNA damage repair (DDR) and cell proliferation. To prevent further confusions, we renamed this protein as TWH19 (Tandem Winged Helix protein formerly known as STK19).


  • Organizational Affiliation
    • Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Serine/threonine-protein kinase 19
A, B
232Homo sapiensMutation(s): 0 
Gene Names: STK19G11RP1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49842 (Homo sapiens)
Explore P49842 
Go to UniProtKB:  P49842
PHAROS:  P49842
GTEx:  ENSG00000204344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49842
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.33α = 90
b = 96.62β = 90
c = 98.83γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2023-06-07 
  • Deposition Author(s): Sun, Q., Li, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-02-26
    Changes: Database references