6AUN | pdb_00006aun

calcium-independent phospholipase A2 beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 
    0.310 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6AUN

This is version 1.4 of the entry. See complete history

Literature

The structure of iPLA2beta reveals dimeric active sites and suggests mechanisms of regulation and localization.

Malley, K.R.Koroleva, O.Miller, I.Sanishvili, R.Jenkins, C.M.Gross, R.W.Korolev, S.

(2018) Nat Commun 9: 765-765

  • DOI: https://doi.org/10.1038/s41467-018-03193-0
  • Primary Citation Related Structures: 
    6AUN

  • PubMed Abstract: 

    Calcium-independent phospholipase A 2 β (iPLA 2 β) regulates important physiological processes including inflammation, calcium homeostasis and apoptosis. It is genetically linked to neurodegenerative disorders including Parkinson's disease. Despite its known enzymatic activity, the mechanisms underlying iPLA 2 β-induced pathologic phenotypes remain poorly understood. Here, we present a crystal structure of iPLA 2 β that significantly revises existing mechanistic models. The catalytic domains form a tight dimer. They are surrounded by ankyrin repeat domains that adopt an outwardly flared orientation, poised to interact with membrane proteins. The closely integrated active sites are positioned for cooperative activation and internal transacylation. The structure and additional solution studies suggest that both catalytic domains can be bound and allosterically inhibited by a single calmodulin. These features suggest mechanisms of iPLA 2 β cellular localization and activity regulation, providing a basis for inhibitor development. Furthermore, the structure provides a framework to investigate the role of neurodegenerative mutations and the function of iPLA 2 β in the brain.


  • Organizational Affiliation
    • Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.

Macromolecule Content 

  • Total Structure Weight: 167.93 kDa 
  • Atom Count: 9,396 
  • Modeled Residue Count: 1,236 
  • Deposited Residue Count: 1,504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PLA2G6, iPLA2beta
A, B
752Cricetulus griseusMutation(s): 0 
EC: 3.1.1.4 (PDB Primary Data), 3.1.2.2 (UniProt), 3.1.1.5 (UniProt)
UniProt
Find proteins for A0A3L7I2I8 (Cricetulus griseus)
Explore A0A3L7I2I8 
Go to UniProtKB:  A0A3L7I2I8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3L7I2I8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free:  0.310 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 266.061α = 90
b = 266.061β = 90
c = 79.375γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR21NS094854
American Heart AssociationUnited States0665513Z
CASISUnited StatesCASIS-2012-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references