6VVG | pdb_00006vvg

Structure of the Cydia pomonella Granulovirus kinase, PK-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.225 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory alpha C helix.

Oliver, M.R.Horne, C.R.Shrestha, S.Keown, J.R.Liang, L.Y.Young, S.N.Sandow, J.J.Webb, A.I.Goldstone, D.C.Lucet, I.S.Kannan, N.Metcalf, P.Murphy, J.M.

(2021) Nat Commun 12: 1002-1002

  • DOI: https://doi.org/10.1038/s41467-021-21191-7
  • Primary Citation Related Structures: 
    6VVG

  • PubMed Abstract: 

    The life cycle of Baculoviridae family insect viruses depends on the viral protein kinase, PK-1, to phosphorylate the regulatory protein, p6.9, to induce baculoviral genome release. Here, we report the crystal structure of Cydia pomenella granulovirus PK-1, which, owing to its likely ancestral origin among host cell AGC kinases, exhibits a eukaryotic protein kinase fold. PK-1 occurs as a rigid dimer, where an antiparallel arrangement of the αC helices at the dimer core stabilizes PK-1 in a closed, active conformation. Dimerization is facilitated by C-lobe:C-lobe and N-lobe:N-lobe interactions between protomers, including the domain-swapping of an N-terminal helix that crowns a contiguous β-sheet formed by the two N-lobes. PK-1 retains a dimeric conformation in solution, which is crucial for catalytic activity. Our studies raise the prospect that parallel, side-to-side dimeric arrangements that lock kinase domains in a catalytically-active conformation could function more broadly as a regulatory mechanism among eukaryotic protein kinases.


  • Organizational Affiliation
    • School of Biological Sciences, University of Auckland, Auckland, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 65.92 kDa 
  • Atom Count: 4,777 
  • Modeled Residue Count: 531 
  • Deposited Residue Count: 558 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginine kinase
A, B
279Cydia pomonella granulosis virus (isolate Mexican)Mutation(s): 0 
Gene Names: orf3
UniProt
Find proteins for A0A097P1P8 (Cydia pomonella granulosis virus)
Explore A0A097P1P8 
Go to UniProtKB:  A0A097P1P8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097P1P8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.225 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.937α = 90
b = 115.37β = 90
c = 119.395γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
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: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description