3IDW | pdb_00003idw

Crystal structure of Sla1 homology domain 2

• PDB DOI: https://doi.org/10.2210/pdb3IDW/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-21 Released: 2010-02-23 
• Deposition Author(s): Di Pietro, S.M., Cascio, D., Bowie, J.U., Payne, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.219 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Regulation of clathrin adaptor function in endocytosis: novel role for the SAM domain.

Di Pietro, S.M., Cascio, D., Feliciano, D., Bowie, J.U., Payne, G.S.

(2010) EMBO J 29: 1033-1044

• PubMed: 20150898 
• DOI: https://doi.org/10.1038/emboj.2010.5
• Primary Citation Related Structures: 
  3IDW


• PubMed Abstract: 
  

  During clathrin-mediated endocytosis, adaptor proteins play central roles in coordinating the assembly of clathrin coats and cargo selection. Here we characterize the binding of the yeast endocytic adaptor Sla1p to clathrin through a variant clathrin-binding motif that is negatively regulated by the Sla1p SHD2 domain. The crystal structure of SHD2 identifies the domain as a sterile alpha-motif (SAM) domain and shows a propensity to oligomerize. By co-immunoprecipitation, Sla1p binds to clathrin and self-associates in vivo. Mutations in the clathrin-binding motif that abolish clathrin binding and structure-based mutations in SHD2 that impede self-association result in endocytosis defects and altered dynamics of Sla1p assembly at the sites of endocytosis. These results define a novel mechanism for negative regulation of clathrin binding by an adaptor and suggest a role for SAM domains in clathrin-mediated endocytosis.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 8.59 kDa 
• Atom Count: 576 
• Modeled Residue Count: 66 
• Deposited Residue Count: 72 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin cytoskeleton-regulatory complex protein SLA1	A	72	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SLA1, YBL007C, YBL0321
UniProt
Find proteins for P32790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32790  Go to UniProtKB:  P32790

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.219 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.273	α = 90
b = 59.273	β = 90
c = 47.54	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Di Pietro, S.M., Cascio, D., Bowie, J.U., Payne, G.S.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references