4A6F

Crystal structure of Slm1-PH domain in complex with Phosphoserine

• PDB DOI: https://doi.org/10.2210/pdb4A6F/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2011-11-02 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: 1.68 Å
• R-Value Free: 0.242 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 

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: 28.46 kDa 
• Atom Count: 1,962 
• Modelled Residue Count: 215 
• Deposited Residue Count: 240 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1	B	120	Saccharomyces cerevisiae	Mutation(s): 0  Membrane Entity: Yes
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
SEP	D [auth A], E [auth A], G [auth B], H [auth B]	PHOSPHOSERINE C3 H8 N O6 P BZQFBWGGLXLEPQ-REOHCLBHSA-N
PO4	C [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.242 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.54	α = 90
b = 73.65	β = 90
c = 82.47	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: 2013-02-06
  Changes: Atomic model
• Version 1.2: 2019-10-16
  Changes: Data collection, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description