6BYR

Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structures of the PKA RI alpha Holoenzyme with the FLHCC Driver J-PKAc alpha or Wild-Type PKAc alpha.

Cao, B.Lu, T.W.Martinez Fiesco, J.A.Tomasini, M.Fan, L.Simon, S.M.Taylor, S.S.Zhang, P.

(2019) Structure 27: 816

  • DOI: https://doi.org/10.1016/j.str.2019.03.001
  • Primary Citation of Related Structures:  
    6BYR, 6BYS

  • PubMed Abstract: 

    Fibrolamellar hepatocellular carcinoma (FLHCC) is driven by J-PKAcα, a kinase fusion chimera of the J domain of DnaJB1 with PKAcα, the catalytic subunit of protein kinase A (PKA). Here we report the crystal structures of the chimeric fusion RIα 2 :J-PKAcα 2 holoenzyme formed by J-PKAcα and the PKA regulatory (R) subunit RIα, and the wild-type (WT) RIα 2 :PKAcα 2 holoenzyme. The chimeric and WT RIα holoenzymes have quaternary structures different from the previously solved WT RIβ and RIIβ holoenzymes. The WT RIα holoenzyme showed the same configuration as the chimeric RIα 2 :J-PKAcα 2 holoenzyme and a distinct second conformation. The J domains are positioned away from the symmetrical interface between the two RIα:J-PKAcα heterodimers in the chimeric fusion holoenzyme and are highly dynamic. The structural and dynamic features of these holoenzymes enhance our understanding of the fusion chimera protein J-PKAcα that drives FLHCC as well as the isoform specificity of PKA.


  • Organizational Affiliation

    Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera
A, C
405Homo sapiensMutation(s): 0 
Gene Names: DNAJB1DNAJ1HDJ1HSPF1PRKACAPKACA
EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
PHAROS:  P17612
GTEx:  ENSG00000072062 
Find proteins for P25685 (Homo sapiens)
Explore P25685 
Go to UniProtKB:  P25685
PHAROS:  P25685
GTEx:  ENSG00000132002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP17612P25685
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase type I-alpha regulatory subunit
B, D
379Bos taurusMutation(s): 0 
Gene Names: PRKAR1A
UniProt
Find proteins for P00514 (Bos taurus)
Explore P00514 
Go to UniProtKB:  P00514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00514
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.504α = 90
b = 166.504β = 90
c = 332.701γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary