6WQX

Human PRPK-TPRKB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the human PRPK-TPRKB complex.

Li, J.Ma, X.Banerjee, S.Chen, H.Ma, W.Bode, A.M.Dong, Z.

(2021) Commun Biol 4: 167-167

  • DOI: https://doi.org/10.1038/s42003-021-01683-4
  • Primary Citation of Related Structures:  
    6WQX

  • PubMed Abstract: 

    Mutations of the p53-related protein kinase (PRPK) and TP53RK-binding protein (TPRKB) cause Galloway-Mowat syndrome (GAMOS) and are found in various human cancers. We have previously shown that small compounds targeting PRPK showed anti-cancer activity against colon and skin cancer. Here we present the 2.53 Å crystal structure of the human PRPK-TPRKB-AMPPNP (adenylyl-imidodiphosphate) complex. The structure reveals details in PRPK-AMPPNP coordination and PRPK-TPRKB interaction. PRPK appears in an active conformation, albeit lacking the conventional kinase activation loop. We constructed a structural model of the human EKC/KEOPS complex, composed of PRPK, TPRKB, OSGEP, LAGE3, and GON7. Disease mutations in PRPK and TPRKB are mapped into the structure, and we show that one mutation, PRPK K238Nfs*2, lost the binding to OSGEP. Our structure also makes the virtual screening possible and paves the way for more rational drug design.


  • Organizational Affiliation

    The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TPRKBA [auth B],
C [auth A]
179Homo sapiensMutation(s): 0 
Gene Names: TPRKBCGI-121My019
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C4 (Homo sapiens)
Explore Q9Y3C4 
Go to UniProtKB:  Q9Y3C4
PHAROS:  Q9Y3C4
GTEx:  ENSG00000144034 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3C4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TP53RKB [auth C],
D
267Homo sapiensMutation(s): 0 
Gene Names: TP53RKC20orf64PRPK
EC: 3.6 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S44 (Homo sapiens)
Explore Q96S44 
Go to UniProtKB:  Q96S44
PHAROS:  Q96S44
GTEx:  ENSG00000172315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96S44
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.856α = 90
b = 77.54β = 106.814
c = 100.413γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description