2J3T | pdb_00002j3t

The crystal structure of the bet3-trs33-bet5-trs23 complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.249 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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.Raunser, S.Munger, C.Wagner, J.Song, Y.Cygler, M.Walz, T.Oh, B.Sacher, M.

(2006) Cell 127: 817

  • DOI: https://doi.org/10.1016/j.cell.2006.09.029
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 79.6 kDa 
  • Atom Count: 5,396 
  • Modeled Residue Count: 665 
  • Deposited Residue Count: 705 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3182Mus musculusMutation(s): 0 
UniProt
Find proteins for O55013 (Mus musculus)
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Go to UniProtKB:  O55013
Entity Groups
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UniProt GroupO55013
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6A159Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75865 (Homo sapiens)
Explore O75865 
Go to UniProtKB:  O75865
PHAROS:  O75865
GTEx:  ENSG00000007255 
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UniProt GroupO75865
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 1145Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5NCF2 (Mus musculus)
Explore Q5NCF2 
Go to UniProtKB:  Q5NCF2
IMPC:  MGI:1098727
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UniProt GroupQ5NCF2
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 4219Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y296 (Homo sapiens)
Explore Q9Y296 
Go to UniProtKB:  Q9Y296
PHAROS:  Q9Y296
GTEx:  ENSG00000196655 
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UniProt GroupQ9Y296
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM

Query on PLM



Download:Ideal Coordinates CCD File
E [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.249 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.602α = 90
b = 66.336β = 90
c = 200.808γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2006-11-22 
  • Deposition Author(s): Kim, Y., Oh, B.

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-22
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary