2CFH

Structure of the Bet3-TPC6B core of TRAPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Bet3-Tpc6B Core of Trapp: Two Tpc6 Paralogs Form Trimeric Complexes with Bet3 and Mum2.

Kummel, D.Muller, J.J.Roske, Y.Henke, N.Heinemann, U.

(2006) J.Mol.Biol. 361: 22

  • DOI: 10.1016/j.jmb.2006.06.012

  • PubMed Abstract: 
  • The transport protein particle (TRAPP) complexes are involved in the tethering process at different trafficking steps of vesicle transport. We here present the crystal structure of a human Bet3-Tpc6B heterodimer, which represents a core sub-complex i ...

    The transport protein particle (TRAPP) complexes are involved in the tethering process at different trafficking steps of vesicle transport. We here present the crystal structure of a human Bet3-Tpc6B heterodimer, which represents a core sub-complex in the assembly of TRAPP. We describe a conserved patch of Tpc6 with uncharged pockets, forming a putative interaction interface for an anchoring moiety at the Golgi. The structural and functional comparison of the two paralogs Tpc6A and Tpc6B, only found in some organisms, indicates redundancy and added complexity of TRAPP architecture and function. Both iso-complexes, Bet3-Tpc6A and Bet3-Tpc6B, are able to recruit Mum2, a further TRAPP subunit, and we identify the alpha1-alpha2 loop regions as a binding site for Mum2. Our study reveals similar stability of the iso-complexes and similar expression patterns of the tpc6 variants in different mouse organs. These findings raise the possibility that the Tpc6 paralogs might contribute to the formation of two distinct TRAPP complexes that differ in function.


    Organizational Affiliation

    Max-Delbrück Center for Molecular Medicine, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
A, B
194Homo sapiensMutation(s): 0 
Gene Names: TRAPPC3 (BET3)
Find proteins for O43617 (Homo sapiens)
Go to Gene View: TRAPPC3
Go to UniProtKB:  O43617
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
C, D
158Homo sapiensMutation(s): 0 
Gene Names: TRAPPC6B
Find proteins for Q86SZ2 (Homo sapiens)
Go to Gene View: TRAPPC6B
Go to UniProtKB:  Q86SZ2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download SDF File 
Download CCD File 
A, B
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.450α = 90.00
b = 69.590β = 91.55
c = 144.006γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-10-26
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary