3GPE | pdb_00003gpe

Crystal Structure Analysis of PKC (alpha)-C2 domain complexed with Ca2+ and PtdIns(4,5)P2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.277 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structural and mechanistic insights into the association of PKCalpha-C2 domain to PtdIns(4,5)P2.

Guerrero-Valero, M.Ferrer-Orta, C.Querol-Audi, J.Marin-Vicente, C.Fita, I.Gomez-Fernandez, J.C.Verdaguer, N.Corbalan-Garcia, S.

(2009) Proc Natl Acad Sci U S A 106: 6603-6607

  • DOI: https://doi.org/10.1073/pnas.0813099106
  • Primary Citation Related Structures: 
    3GPE

  • PubMed Abstract: 

    C2 domains are widely-spread protein signaling motifs that in classical PKCs act as Ca(2+)-binding modules. However, the molecular mechanisms of their targeting process at the plasma membrane remain poorly understood. Here, the crystal structure of PKCalpha-C2 domain in complex with Ca(2+), 1,2-dihexanoyl-sn-glycero-3-[phospho-L-serine] (PtdSer), and 1,2-diayl-sn-glycero-3-[phosphoinositol-4,5-bisphosphate] [PtdIns(4,5)P(2)] shows that PtdSer binds specifically to the calcium-binding region, whereas PtdIns(4,5)P(2) occupies the concave surface of strands beta3 and beta4. Strikingly, the structure reveals a PtdIns(4,5)P(2)-C2 domain-binding mode in which the aromatic residues Tyr-195 and Trp-245 establish direct interactions with the phosphate moieties of the inositol ring. Mutations that abrogate Tyr-195 and Trp-245 recognition of PtdIns(4,5)P(2) severely impaired the ability of PKCalpha to localize to the plasma membrane. Notably, these residues are highly conserved among C2 domains of topology I, and a general mechanism of C2 domain-membrane docking mediated by PtdIns(4,5)P(2) is presented.


  • Organizational Affiliation
    • Department of Bioquímica y Biología Molecular A, Facultad de Veterinaria, Universidad de Murcia, 30100 Murcia, Spain.

Macromolecule Content 

  • Total Structure Weight: 17.31 kDa 
  • Atom Count: 1,248 
  • Modeled Residue Count: 137 
  • Deposited Residue Count: 137 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein kinase C alpha type137Rattus norvegicusMutation(s): 0 
Gene Names: PrkcaPkca
EC: 2.7.11.13
UniProt
Find proteins for P05696 (Rattus norvegicus)
Explore P05696 
Go to UniProtKB:  P05696
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05696
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.277 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.848α = 90
b = 57.848β = 90
c = 90.479γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-04-03
    Changes: Refinement description