1I3S | pdb_00001i3s

THE 2.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.258 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Crystal structure of baculovirus P35 reveals a novel conformational change in the reactive site loop after caspase cleavage.

dela Cruz, W.P.Friesen, P.D.Fisher, A.J.

(2001) J Biological Chem 276: 32933-32939

  • DOI: https://doi.org/10.1074/jbc.M103930200
  • Primary Citation Related Structures: 
    1I3P, 1I3S

  • PubMed Abstract: 

    Baculovirus P35 is a universal suppressor of apoptosis that stoichiometrically inhibits cellular caspases in a novel cleavage-dependent mechanism. Upon caspase cleavage at Asp-87, the 10- and 25-kDa cleavage products of P35 remain tightly associated with the inhibited caspase. Mutations in the alpha-helix of the reactive site loop preceding the cleavage site abrogate caspase inhibition and antiapoptotic activity. Substitution of Pro for Val-71, which is located in the middle of this alpha-helix, produces a protein that is cleaved at the requisite Asp-87 but does not remain bound to the caspase. This loss-of-function mutation provided the opportunity to structurally analyze the conformational changes of the P35 reactive site loop after caspase cleavage. We report here the 2.7 A resolution crystal structure of V71P-mutated P35 after cleavage by human caspase-3. The structure reveals a large movement in the carboxyl-terminal side of the reactive site loop that swings down and forms a new beta-strand that augments an existing beta-sheet. Additionally, the hydrophobic amino terminus releases and extends away from the protein core. Similar movements occur when P35 forms an inhibitory complex with human caspase-8. These findings suggest that the alpha-helix mutation may alter the sequential steps or kinetics of the conformational changes required for inhibition, thereby causing P35 loss of function.


  • Organizational Affiliation
    • Department of Chemistry, University of California, Davis, California 95616, USA.

Macromolecule Content 

  • Total Structure Weight: 104.69 kDa 
  • Atom Count: 6,781 
  • Modeled Residue Count: 846 
  • Deposited Residue Count: 894 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EARLY 35 KDA PROTEIN
A, B, C
298Autographa californica nucleopolyhedrovirusMutation(s): 1 
Gene Names: P35
UniProt
Find proteins for P08160 (Autographa californica nuclear polyhedrosis virus)
Explore P08160 
Go to UniProtKB:  P08160
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08160
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.258 (Depositor) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.608α = 90
b = 89.303β = 90
c = 136.099γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-09
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary