5V7V Protein Transport date Mar 20, 2017
title Cryo-Em Structure Of Erad-Associated E3 Ubiquitin-Protein Li Component Hrd3
authors W.Mi, S.Schoebel, A.Stein, T.A.Rapoport, M.Liao
compound source
Molecule: Erad-Associated E3 Ubiquitin-Protein Ligase Compo
Chain: A
Fragment: Unp Residues 1-767
Synonym: Hmg-Coa Reductase Degradation Protein 3
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Hrd3, Ylr207w
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.90 Å
ligand BMA, NAG enzyme
Primary referenceCryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3., Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M, Nature. 2017 Aug 17;548(7667):352-355. doi: 10.1038/nature23314. Epub 2017 Jul 6. PMID:28682307
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (180 Kb) [Save to disk]
  • Biological Unit Coordinates (5v7v.pdb1.gz) 173 Kb
  • LPC: Ligand-Protein Contacts for 5V7V
  • CSU: Contacts of Structural Units for 5V7V
  • Retrieve 5V7V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V7V from S2C, [Save to disk]
    • View 5V7V 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 5V7V
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v7v_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5V7V
  • Community annotation for 5V7V at PDBWiki (http://pdbwiki.org)

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