3DKN Protein Transport Rna date Jun 25, 2008
title Sec61 In The Canine Ribosome-Channel Complex From The Endopl Reticulum
authors J.F.Menetret, C.Akey
compound source
Molecule: Rna (5'- R(Pcpgpupgpcpcpapapgpcpupgpcpgpapupapapg
Chain: D
Other_details: Helix 6
 Organism_scientific: Canis Lupus Familiaris
Organism_taxid: 9615

Molecule: Rna (5'- R(Papgpcpcpgpcpapcpgpgpapgpgpcpgpapa)-3');
Chain: E
Other_details: Helix 7
Organism_scientific: Canis Lupus Familiaris
Organism_taxid: 9615

Molecule: Rna (32-Mer)
Chain: F
Other_details: Helix 50
Organism_scientific: Canis Lupus Familiaris
Organism_taxid: 9615

Molecule: Preprotein Translocase Subunit Secy
Chain: A
Synonym: Protein Transport Protein Sec61 Subunit Alpha Homo
Organism_scientific: Canis Lupus Familiaris
Organism_taxid: 9615

Molecule: Preprotein Translocase Subunit Sece
Chain: B
Synonym: Protein Transport Protein Sec61 Gamma Subunit Homo
Organism_scientific: Canis Lupus Familiaris
Organism_taxid: 9615

Molecule: Preprotein Translocase Subunit Secg
Chain: C
Synonym: Protein Transport Protein Sec61 Subunit Beta Homol
Organism_scientific: Canis Lupus Familiaris
Organism_taxid: 9615
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 8.70 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceSingle copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome., Menetret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW, Structure. 2008 Jul;16(7):1126-37. PMID:18611385
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (3dkn.pdb1.gz) 106 Kb
  • CSU: Contacts of Structural Units for 3DKN
  • Likely Quarternary Molecular Structure file(s) for 3DKN
  • Retrieve 3DKN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DKN from S2C, [Save to disk]
    • View 3DKN 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 3DKN
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3DKN, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dkn_E] [3dkn_F] [3dkn] [3dkn_D] [3dkn_B] [3dkn_C] [3dkn_A]
  • SWISS-PROT database: [Q57817] [P60460] [Q60175]
  • Belongs to the general secretory pathway (sec) family according to TCDB.
  • Domain organization of [SECE_METJA] [SECG_METJA] [SECY_METJA] by SWISSPFAM
    • Other resources with information on 3DKN
  • Community annotation for 3DKN 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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