3PVB | pdb_00003pvb

Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.290 (Depositor), 0.341 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.274 (DCC) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase

Boettcher, A.J.Wu, J.Kim, C.Yang, J.Bruystens, J.Cheung, N.Pennypacker, J.K.Blumenthal, D.A.Kornev, A.P.Taylor, S.S.

(2011) Structure 19: 265-276

  • DOI: https://doi.org/10.1016/j.str.2010.12.005
  • Primary Citation Related Structures: 
    3PVB

  • PubMed Abstract: 

    PKA holoenzymes containing two catalytic (C) subunits and a regulatory (R) subunit dimer are activated cooperatively by cAMP. While cooperativity involves the two tandem cAMP binding domains in each R-subunit, additional cooperativity is associated with the tetramer. Of critical importance is the flexible linker in R that contains an inhibitor site (IS). While the IS becomes ordered in the R:C heterodimer, the overall conformation of the tetramer is mediated largely by the N-Linker that connects the D/D domain to the IS. To understand how the N-Linker contributes to assembly of tetrameric holoenzymes, we engineered a monomeric RIα that contains most of the N-Linker, RIα(73-244), and crystallized a holoenzyme complex. Part of the N-linker is now ordered by interactions with a symmetry-related dimer. This complex of two symmetry-related dimers forms a tetramer that reveals novel mechanisms for allosteric regulation and has many features associated with full-length holoenzyme. A model of the tetrameric holoenzyme, based on this structure, is consistent with previous small angle X-ray and neutron scattering data, and is validated with new SAXS data and with an RIα mutation localized to a novel interface unique to the tetramer.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.

Macromolecule Content 

  • Total Structure Weight: 59.05 kDa 
  • Atom Count: 4,046 
  • Modeled Residue Count: 505 
  • Deposited Residue Count: 505 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alpha345Mus musculusMutation(s): 0 
Gene Names: PrkacaPkaca
EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus)
Explore P05132 
Go to UniProtKB:  P05132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05132
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase type I-alpha regulatory subunit160Bos 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: 3.30 Å
  • R-Value Free:  0.290 (Depositor), 0.341 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.274 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.667α = 90
b = 116.667β = 90
c = 140.103γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary