4A6H

Crystal structure of Slm1-PH domain in complex with Inositol-4- phosphate

• PDB DOI: https://doi.org/10.2210/pdb4A6H/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2011-11-03 Released: 2012-06-13 
• Deposition Author(s): Anand, K., Maeda, K., Gavin, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Structural Analyses of Slm1-Ph Domain Demonstrate Ligand Binding in the Non-Canonical Site

Anand, K., Maeda, K., Gavin, A.C.

(2012) PLoS One 7: 36526

• PubMed: 22574179 
• DOI: https://doi.org/10.1371/journal.pone.0036526
• Primary Citation of Related Structures:  
  4A5K, 4A6F, 4A6H, 4A6K


• PubMed Abstract: 
  

  Pleckstrin homology (PH) domains are common membrane-targeting modules and their best characterized ligands are a set of important signaling lipids that include phosphatidylinositol phosphates (PtdInsPs). PH domains recognize PtdInsPs through two distinct mechanisms that use different binding pockets on opposite sides of the β-strands 1 and 2: i) a canonical binding site delimited by the β1-β2 and β3-β4loops and ii) a non-canonical binding site bordered by the β1-β2 and β5-β6loops. The PH domain-containing protein Slm1 from budding yeast Saccharomyces cerevisiae is required for actin cytoskeleton polarization and cell growth. We recently reported that this PH domain binds PtdInsPs and phosphorylated sphingolipids in a cooperative manner.

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Organizational Affiliation: 

European Molecular Biology Laboratory Heidelberg, Structural and Computational Biology Unit, Heidelberg, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.65 kDa 
• Atom Count: 3,965 
• Modelled Residue Count: 429 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1	A, B, C, D	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40485 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40485  Go to UniProtKB:  P40485

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I4D	G [auth A], H [auth A], L [auth B]	D-MYO-INOSITOL-4-PHOSPHATE C6 H13 O9 P INAPMGSXUVUWAF-CNWJWELYSA-N
PO4	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth D], O [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37	α = 90
b = 71.6	β = 90
c = 82.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Anand, K., Maeda, K., Gavin, A.C.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2015-03-25
  Changes: Atomic model, Derived calculations, Non-polymer description, Other