3G9H | pdb_00003g9h

Crystal structure of the C-terminal mu homology domain of Syp1

• PDB DOI: https://doi.org/10.2210/pdb3G9H/pdb

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


• Deposited: 2009-02-13 Released: 2009-09-22 
• Deposition Author(s): Reider, A., Barker, S., Mishra, S., Im, Y.J., Maldonado-Baez, L., Hurley, J., Traub, L., Wendland, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Syp1 is a conserved endocytic adaptor that contains domains involved in cargo selection and membrane tubulation.

Reider, A., Barker, S.L., Mishra, S.K., Im, Y.J., Maldonado-Baez, L., Hurley, J.H., Traub, L.M., Wendland, B.

(2009) EMBO J 28: 3103-3116

• PubMed: 19713939 
• DOI: https://doi.org/10.1038/emboj.2009.248
• Primary Citation Related Structures: 
  3G9G, 3G9H


• PubMed Abstract: 
  

  Internalization of diverse transmembrane cargos from the plasma membrane requires a similarly diverse array of specialized adaptors, yet only a few adaptors have been characterized. We report the identification of the muniscin family of endocytic adaptors that is conserved from yeast to human beings. Solving the structures of yeast muniscin domains confirmed the unique combination of an N-terminal domain homologous to the crescent-shaped membrane-tubulating EFC/F-BAR domains and a C-terminal domain homologous to cargo-binding mu homology domains (muHDs). In vitro and in vivo assays confirmed membrane-tubulation activity for muniscin EFC/F-BAR domains. The muHD domain has conserved interactions with the endocytic adaptor/scaffold Ede1/eps15, which influences muniscin localization. The transmembrane protein Mid2, earlier implicated in polarized Rho1 signalling, was identified as a cargo of the yeast adaptor protein. These and other data suggest a model in which the muniscins provide a combined adaptor/membrane-tubulation activity that is important for regulating endocytosis.

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Organizational Affiliation: 
• Department of Biology, The Johns Hopkins University, Baltimore, MD 21218-2685, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.94 kDa 
• Atom Count: 2,050 
• Modeled Residue Count: 262 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Suppressor of yeast profilin deletion	A	328	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SYP1, YCR030C, YCR30C/YCR29C
UniProt
Find proteins for P25623 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25623  Go to UniProtKB:  P25623

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	B [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.063	α = 90
b = 134.063	β = 90
c = 93.703	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Reider, A., Barker, S., Mishra, S., Im, Y.J., Maldonado-Baez, L., Hurley, J., Traub, L., Wendland, B.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations