3ULC | pdb_00003ulc

Crystal structure of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1, a TORC2 subunit, in the P3121 crystal form

• PDB DOI: https://doi.org/10.2210/pdb3ULC/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-10 Released: 2012-04-11 
• Deposition Author(s): Pan, D., Matsuura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.289 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2

Pan, D., Matsuura, Y.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 386-392

• PubMed: 22505404 
• DOI: https://doi.org/10.1107/S1744309112007178
• Primary Citation Related Structures: 
  3ULB, 3ULC, 3VOQ


• PubMed Abstract: 
  

  In eukaryotes, multiprotein complexes termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2) function as major regulators of cell growth, metabolism and ageing. The C-terminal domain of the Saccharomyces cerevisiae TORC2 component Avo1 is required for plasma-membrane localization of TORC2 and is essential for yeast viability. X-ray crystal structures of the C-terminal domain of Avo1 and of its human orthologue Sin1 have been determined. The structures show that the C-termini of Avo1 and Sin1 both have the pleckstrin homology (PH) domain fold. Comparison with known PH-domain structures suggests a putative binding site for phosphoinositides.

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Organizational Affiliation: 
• Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 14.61 kDa 
• Atom Count: 808 
• Modeled Residue Count: 100 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Target of rapamycin complex 2 subunit AVO1	A	121	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: AVO1
UniProt
Find proteins for Q08236 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08236  Go to UniProtKB:  Q08236

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.289 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.917	α = 90
b = 60.917	β = 90
c = 84.096	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Pan, D., Matsuura, Y.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description