2J3R | pdb_00002j3r

The crystal structure of the bet3-trs31 heterodimer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLMClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

The Architecture of the Multisubunit Trapp I Complex Suggests a Model for Vesicle Tethering.

Kim, Y.-G.Raunser, S.Munger, C.Wagner, J.Song, Y.-L.Cygler, M.Walz, T.Oh, B.-H.Sacher, M.

(2006) Cell 127: 817

  • DOI: https://doi.org/10.1016/j.cell.2006.09.029
  • Primary Citation of Related Structures:  
    2J3R, 2J3T, 2J3W

  • PubMed Abstract: 

    Transport protein particle (TRAPP) I is a multisubunit vesicle tethering factor composed of seven subunits involved in ER-to-Golgi trafficking. The functional mechanism of the complex and how the subunits interact to form a functional unit are unknown. Here, we have used a multidisciplinary approach that includes X-ray crystallography, electron microscopy, biochemistry, and yeast genetics to elucidate the architecture of TRAPP I. The complex is organized through lateral juxtaposition of the subunits into a flat and elongated particle. We have also localized the site of guanine nucleotide exchange activity to a highly conserved surface encompassing several subunits. We propose that TRAPP I attaches to Golgi membranes with its large flat surface containing many highly conserved residues and forms a platform for protein-protein interactions. This study provides the most comprehensive view of a multisubunit vesicle tethering complex to date, based on which a model for the function of this complex, involving Rab1-GTP and long, coiled-coil tethers, is presented.


  • Organizational Affiliation

    Center for Biomolecular Recognition and Division of Molecular and Life Sciences, Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3182Mus musculusMutation(s): 0 
UniProt
Find proteins for O55013 (Mus musculus)
Explore O55013 
Go to UniProtKB:  O55013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO55013
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ZGC 92866157Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6DGL5 (Danio rerio)
Explore Q6DGL5 
Go to UniProtKB:  Q6DGL5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DGL5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.492α = 90
b = 93.348β = 92.41
c = 60.988γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-27
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary