3APQ Oxidoreductase date Oct 20, 2010
title Crystal Structure Of J-Trx1 Fragment Of Erdj5
authors K.Inaba, M.Suzuki, K.Nagata
compound source
Molecule: Dnaj Homolog Subfamily C Member 10
Chain: A, B
Fragment: J-Trx1 Domain (Unp Residues 34-242)
Synonym: Er-Resident Protein Erdj5, Endoplasmic Reticulum D Fusion Protein 1, J Domain-Containing Protein Disulfide Iso Like Protein, J Domain-Containing Pdi-Like Protein, Jpdi;
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Dnajc10, Erdj5, Jpdi
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-5x
symmetry Space Group: P 1 21 1
R_factor 0.170 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.008 61.179 62.912 90.00 106.34 90.00
method X-Ray Diffractionresolution 1.84 Å
Primary referenceStructural basis of an ERAD pathway mediated by the ER-resident protein disulfide reductase ERdj5., Hagiwara M, Maegawa K, Suzuki M, Ushioda R, Araki K, Matsumoto Y, Hoseki J, Nagata K, Inaba K, Mol Cell. 2011 Feb 18;41(4):432-44. PMID:21329881
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (3apq.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (3apq.pdb2.gz) 73 Kb
  • CSU: Contacts of Structural Units for 3APQ
  • Structure Factors (494 Kb)
  • Retrieve 3APQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3APQ from S2C, [Save to disk]
  • Re-refined 3apq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3APQ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3APQ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3APQ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3apq_B] [3apq] [3apq_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3APQ: [DnaJ ] by SMART
    • Other resources with information on 3APQ
  • Community annotation for 3APQ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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