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 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 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 ...

    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

    China-US (Henan) Hormel Cancer Institute, Zhengzhou, China. dongzg@zzu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TPRKB AB179Homo sapiensMutation(s): 0 
Gene Names: TPRKBCGI-121My019
Find proteins for Q9Y3C4 (Homo sapiens)
Explore Q9Y3C4 
Go to UniProtKB:  Q9Y3C4
NIH Common Fund Data Resources
PHAROS:  Q9Y3C4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TP53RK CD267Homo sapiensMutation(s): 0 
Gene Names: TP53RKC20orf64PRPK
EC: 3.6 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for Q96S44 (Homo sapiens)
Explore Q96S44 
Go to UniProtKB:  Q96S44
NIH Common Fund Data Resources
PHAROS:  Q96S44
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release