9S9T | pdb_00009s9t

Structure of human PKCBeta Kinase domain with Ruboxistaurin, D427N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 
    0.290 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.215 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Penetrant PKCb mutation in ATLL displays a mixed gain-of-function.

Brown, S.J.L.Briggs, D.C.Costello, P.Yaguchi, H.Bangham, C.R.M.Parker, P.J.McDonald, N.Q.

(2025) Biochem J 

  • DOI: https://doi.org/10.1042/BCJ20253384
  • Primary Citation of Related Structures:  
    9S9T

  • PubMed Abstract: 

    Mutations in the T-cell receptor signalling pathway have been identified in patients with adult T-cell leukaemia/lymphoma (ATLL) and one of the most frequently observed targets of these mutations is protein kinase C beta (PKCb). Here we have characterised the most frequent mutation in PKCb (D427N) addressing the issue of gain/loss of function, neomorphic change, assessing the impact of mutation in vivo, in cells, biochemically and structurally. It is concluded that this mutation is a gain-of-function, activating mutation that confers an altered substrate specificity on this protein kinase. In a constitutive knock-in mouse model this activated allele induces splenomegaly associated with extramedullary haematopoiesis. Pharmacologically, the D427N mutant protein displays poor sensitivity to established PKCb inhibitors, necessitating development of bespoke therapeutics for any ATLL intervention through this target. Such efforts could be guided by the availability the D427N mutant-ruboxistaurin structure presented here.


  • Organizational Affiliation
    • Protein Phosphorylation Laboratory, Midland Road, London, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Beta-II of Protein kinase C beta type353Homo sapiensMutation(s): 1 
Gene Names: PRKCBPKCBPRKCB1
EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P05771 (Homo sapiens)
Go to UniProtKB:  P05771
PHAROS:  P05771
GTEx:  ENSG00000166501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05771-2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LY4 (Subject of Investigation/LOI)
Query on LY4

Download Ideal Coordinates CCD File 
B [auth A](9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE
C28 H28 N4 O3
ZCBUQCWBWNUWSU-SFHVURJKSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free:  0.290 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.215 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.327α = 90
b = 102.327β = 90
c = 82.827γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
gemmidata extraction
DIALSdata scaling
MrBUMPphasing
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomCC2068

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release