1CJY | pdb_00001cjy

HUMAN CYTOSOLIC PHOSPHOLIPASE A2

• PDB DOI: https://doi.org/10.2210/pdb1CJY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1999-04-20 Released: 2000-04-20 
• Deposition Author(s): Dessen, A., Tang, J., Schmidt, H., Stahl, M., Clark, J.D., Seehra, J., Somers, W.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.298 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Crystal structure of human cytosolic phospholipase A2 reveals a novel topology and catalytic mechanism.

Dessen, A., Tang, J., Schmidt, H., Stahl, M., Clark, J.D., Seehra, J., Somers, W.S.

(1999) Cell 97: 349-360

• PubMed: 10319815 
• DOI: https://doi.org/10.1016/s0092-8674(00)80744-8
• Primary Citation Related Structures: 
  1CJY


• PubMed Abstract: 
  

  Cytosolic phospholipase A2 initiates the biosynthesis of prostaglandins, leukotrienes, and platelet-activating factor (PAF), mediators of the pathophysiology of asthma and arthritis. Here, we report the X-ray crystal structure of human cPLA2 at 2.5 A. cPLA2 consists of an N-terminal calcium-dependent lipid-binding/C2 domain and a catalytic unit whose topology is distinct from that of other lipases. An unusual Ser-Asp dyad located in a deep cleft at the center of a predominantly hydrophobic funnel selectively cleaves arachidonyl phospholipids. The structure reveals a flexible lid that must move to allow substrate access to the active site, thus explaining the interfacial activation of this important lipase.

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Organizational Affiliation: 
• Biochemistry, Wyeth Research, Cambridge, Massachusetts 02140, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 171.17 kDa 
• Atom Count: 9,706 
• Modeled Residue Count: 1,247 
• Deposited Residue Count: 1,498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)	A, B	749	Homo sapiens	Mutation(s): 0  EC: 3.1.1.4 (PDB Primary Data), 3.1.1.5 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P47712 (Homo sapiens) Explore P47712  Go to UniProtKB:  P47712
PHAROS:  P47712 GTEx:  ENSG00000116711

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	C [auth A], D [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CA	BindingDB:  1CJY	ΔG: min: -3.32e+1, max: -2.60e+1 (kJ/mol) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.298 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.59	α = 90
b = 95.49	β = 90
c = 139.13	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-20 
Deposition Author(s): Dessen, A., Tang, J., Schmidt, H., Stahl, M., Clark, J.D., Seehra, J., Somers, W.S.

Revision History  

• Version 1.0: 2000-04-20
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations