2FJI | pdb_00002fji

Crystal structure of the C-terminal domain of the exocyst subunit Sec6p

• PDB DOI: https://doi.org/10.2210/pdb2FJI/pdb

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


• Deposited: 2006-01-02 Released: 2006-05-16 
• Deposition Author(s): Sivaram, M.V., Munson, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.251 (DCC) 

Literature

The structure of the exocyst subunit Sec6p defines a conserved architecture with diverse roles.

Sivaram, M.V., Furgason, M.L., Brewer, D.N., Munson, M.

(2006) Nat Struct Mol Biol 13: 555-556

• PubMed: 16699513 
• DOI: https://doi.org/10.1038/nsmb1096
• Primary Citation Related Structures: 
  2FJI


• PubMed Abstract: 
  

  The exocyst is a conserved protein complex essential for trafficking secretory vesicles to the plasma membrane. The structure of the C-terminal domain of the exocyst subunit Sec6p reveals multiple helical bundles, which are structurally and topologically similar to Exo70p and the C-terminal domains of Exo84p and Sec15, despite <10% sequence identity. The helical bundles appear to be evolutionarily related molecular scaffolds that have diverged to create functionally distinct exocyst proteins.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.5 kDa 
• Atom Count: 6,868 
• Modeled Residue Count: 795 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exocyst complex component SEC6	A [auth 1], B [auth 2]	399	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SEC6
UniProt
Find proteins for P32844 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32844  Go to UniProtKB:  P32844

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.251 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.295	α = 90
b = 63.301	β = 103.89
c = 151.468	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Sivaram, M.V., Munson, M.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2024-02-14
  Changes: Advisory, Data collection, Database references