3J46 Ribosome Protein Transport date Jun 18, 2013
title Structure Of The Secy Protein Translocation Channel In Actio
authors C.W.Akey, E.Park, J.F.Menetret, J.C.Gumbart, S.J.Ludtke, W.Li, A.W T.A.Rapoport
compound source
Molecule: Protein Translocase Subunit Secy
Chain: y
Engineered: Yes
Mutation: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ep72
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad(Mazf)-Nc100

Molecule: Preprotein Translocase Subunit Sece
Chain: E
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ep72
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad(Mazf)-Nc100

Molecule: Protein-Export Membrane Protein Secg
Chain: G
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ep72
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad(Mazf)-Nc100

Molecule: Nc100
Chain: n
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ep72
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad(Mazf)-Nc100

Molecule: P-Trna
Chain: p
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: A-Trna
Chain: a
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L1
Chain: 5
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L23p
Chain: T
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L24p
Chain: U
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L29p
Chain: Y
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Ribosomal Rna
Chain: 1
Fragment: Helix 6 - Helix 7
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Ribosomal Rna
Chain: 2
Fragment: Helix 50
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Ribosomal Rna
Chain: 3
Fragment: Helix 59
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Ribosomal Rna
Chain: 4
Fragment: Helix 76 - Helix 78
Organism_scientific: Escherichia Coli
Organism_taxid: 562
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 10.10 Å
ligand ACE, MIA, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
5


E


G


T


U


Y


y


Primary referenceStructure of the SecY channel during initiation of protein translocation., Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW, Nature. 2013 Oct 23. doi: 10.1038/nature12720. PMID:24153188
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (312 Kb) [Save to disk]
  • Biological Unit Coordinates (3j46.pdb1.gz) 304 Kb
  • LPC: Ligand-Protein Contacts for 3J46
  • CSU: Contacts of Structural Units for 3J46
  • Retrieve 3J46 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J46 from S2C, [Save to disk]
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    • Visual 3D analysis of 3J46
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J46, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j46_2] [3j46_n] [3j46_a] [3j46_Y] [3j46_E] [3j46_T] [3j46] [3j46_y] [3j46_U] [3j46_4] [3j46_p] [3j46_1] [3j46_5] [3j46_3] [3j46_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3J46: [KOW ] by SMART
    • Other resources with information on 3J46
  • Community annotation for 3J46 at PDBWiki (http://pdbwiki.org)

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