1MAI | pdb_00001mai

STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM PHOSPHOLIPASE C DELTA IN COMPLEX WITH INOSITOL TRISPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1MAI/pdb

• Classification: SIGNAL TRANSDUCTION PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-05-23 Released: 1996-11-08 
• Deposition Author(s): Ferguson, K.M., Lemmon, M.A., Schlessinger, J., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.291 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain.

Ferguson, K.M., Lemmon, M.A., Schlessinger, J., Sigler, P.B.

(1995) Cell 83: 1037-1046

• PubMed: 8521504 
• DOI: https://doi.org/10.1016/0092-8674(95)90219-8
• Primary Citation Related Structures: 
  1MAI


• PubMed Abstract: 
  

  The X-ray crystal structure of the high affinity complex between the pleckstrin homology (PH) domain from rat phospholipase C-delta 1 (PLC-delta 1) and inositol-(1,4,5)-trisphosphate (Ins(1,4,5)P3) has been refined to 1.9 A resolution. The domain fold is similar to others of known structure. Ins(1,4,5)P3 binds on the positively charged face of the electrostatically polarized domain, interacting predominantly with the beta 1/beta 2 and beta 3/beta 4 loops. The 4- and 5-phosphate groups of Ins(1,4,5)P3 interact much more extensively than the 1-phosphate. Two amino acids in the PLC-delta 1 PH domain that contact Ins(1,4,5)P3 have counterparts in the Bruton's tyrosine kinase (Btk) PH domain, where mutational changes cause inherited agammaglobulinemia, suggesting a mechanism for loss of function in Btk mutants. Using electrostatics and varying levels of head-group specificity, PH domains may localize and orient signaling proteins, providing a general membrane targeting and regulatory function.

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Organizational Affiliation: 
• Department of Chemistry, Yale University, New Haven, Connecticut 06510, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.87 kDa 
• Atom Count: 1,118 
• Modeled Residue Count: 119 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE C DELTA-1	A	131	Rattus norvegicus	Mutation(s): 0  EC: 3.1.4.11
UniProt
Find proteins for P10688 (Rattus norvegicus) Explore P10688  Go to UniProtKB:  P10688

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3P	B [auth A]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C6 H15 O15 P3 MMWCIQZXVOZEGG-XJTPDSDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.291 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.4	α = 90
b = 59.4	β = 90
c = 80.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Ferguson, K.M., Lemmon, M.A., Schlessinger, J., Sigler, P.B.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other