3J45 Ribosome Protein Transport date Jun 18, 2013
title Structure Of A Non-Translocating Secy Protein Channel With T Ribosome
authors J.F.Menetret, E.Park, J.C.Gumbart, S.J.Ludtke, W.Li, A.Whynot, T.A.Rapoport, C.W.Akey
compound source
Molecule: Protein Translocase Subunit Secy
Chain: y
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Secy
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: C43(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad-Ehisyg

Molecule: Preprotein Translocase Subunit Sece
Chain: E
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Sece
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: C43(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad-Ehisyg

Molecule: Protein-Export Membrane Protein Secg
Chain: G
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Secg
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: C43(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad-Ehisyg

Molecule: 50s Ribosomal Protein L23
Chain: T

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 50s Ribosomal Protein L24
Chain: U

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 50s Ribosomal Protein L29
Chain: Y

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 23s Ribosomal Rna
Chain: 1
Fragment: Helix 6 - Helix 7

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 23s Ribosomal Rna
Chain: 2
Fragment: Helix 50

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 23s Ribosomal Rna
Chain: 3
Fragment: Helix 59

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 23s Ribosomal Rna
Chain: 4
Fragment: Helix 68

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 23s Ribosomal Rna
Chain: 5
Fragment: Helix 76 - Helix 78

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600
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 9.50 Å
ligand ACE, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
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] (216 Kb) [Save to disk]
  • Biological Unit Coordinates (3j45.pdb1.gz) 209 Kb
  • LPC: Ligand-Protein Contacts for 3J45
  • CSU: Contacts of Structural Units for 3J45
  • Retrieve 3J45 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J45 from S2C, [Save to disk]
  • View 3J45 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 3J45
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J45, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j45_2] [3j45_3] [3j45_5] [3j45_T] [3j45] [3j45_y] [3j45_4] [3j45_E] [3j45_U] [3j45_G] [3j45_1] [3j45_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3J45: [KOW ] by SMART
  • Other resources with information on 3J45
  • Community annotation for 3J45 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science