3CUE

Crystal structure of a TRAPP subassembly activating the Rab Ypt1p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes.

Cai, Y.Chin, H.F.Lazarova, D.Menon, S.Fu, C.Cai, H.Sclafani, A.Rodgers, D.W.De La Cruz, E.M.Ferro-Novick, S.Reinisch, K.M.

(2008) Cell 133: 1202-1213

  • DOI: 10.1016/j.cell.2008.04.049

  • PubMed Abstract: 
  • The multimeric membrane-tethering complexes TRAPPI and TRAPPII share seven subunits, of which four (Bet3p, Bet5p, Trs23p, and Trs31p) are minimally needed to activate the Rab GTPase Ypt1p in an event preceding membrane fusion. Here, we present the st ...

    The multimeric membrane-tethering complexes TRAPPI and TRAPPII share seven subunits, of which four (Bet3p, Bet5p, Trs23p, and Trs31p) are minimally needed to activate the Rab GTPase Ypt1p in an event preceding membrane fusion. Here, we present the structure of a heteropentameric TRAPPI assembly complexed with Ypt1p. We propose that TRAPPI facilitates nucleotide exchange primarily by stabilizing the nucleotide-binding pocket of Ypt1p in an open, solvent-accessible form. Bet3p, Bet5p, and Trs23p interact directly with Ypt1p to stabilize this form, while the C terminus of Bet3p invades the pocket to participate in its remodeling. The Trs31p subunit does not interact directly with the GTPase but allosterically regulates the TRAPPI interface with Ypt1p. Our findings imply that TRAPPII activates Ypt1p by an identical mechanism. This view of a multimeric membrane-tethering assembly complexed with a Rab provides a framework for understanding events preceding membrane fusion at the molecular level.


    Organizational Affiliation

    Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transport protein particle 23 kDa subunit
A, G, M, S
219Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TRS23
Find proteins for Q03784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transport protein particle 31 kDa subunit
B, H, N, T
283Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TRS31
Find proteins for Q03337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03337
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transport protein particle 18 kDa subunit
C, I, O, U
159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BET5
Find proteins for Q03630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03630
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Transport protein particle 22 kDa subunit
D, E, J, K, P, Q, V, W
193Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BET3
Find proteins for P36149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36149
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein YPT1
F, L, R, X
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YPT1 (YP2)
Find proteins for P01123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P01123
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download SDF File 
Download CCD File 
E, K, Q, W
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 115.120α = 90.00
b = 115.400β = 90.28
c = 290.070γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
SHARPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references