3DEG Ribosome date Jun 10, 2008
title Complex Of Elongating Escherichia Coli 70s Ribosome And Ef4( Gmppnp
authors S.R.Connell, M.Topf, Y.Qin, D.N.Wilson, T.Mielke, P.Fucini, K.H.Ni C.M.T.Spahn
compound source
Molecule: Al-Trna
Chain: A
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: P-Trna
Chain: B

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Rna Helix 8
Chain: E

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Rna Helix 14
Chain: F

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Rna Helix 42-44
Chain: G

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Rna Helix 95
Chain: I

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Rna Helix 71
Chain: J

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Rna Helix 92
Chain: K

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Gtp-Binding Protein Lepa
Chain: C
Fragment: Ef4
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Lepa, B2569, Jw2553
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b

Molecule: 30s Ribosomal Protein S12
Chain: D

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12

Molecule: 50s Ribosomal Protein L11
Chain: H

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
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 10.90 Å
ligand 1MA, 2MG, 5MC, 5MU, 7MG, H2U, M2G, OMC, OMG, PSU, YG enzyme
Gene
Ontology
ChainFunctionProcessComponent
C
  • translation elongation facto...


  • D


    H


    Primary referenceA new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation., Connell SR, Topf M, Qin Y, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CM, Nat Struct Mol Biol. 2008 Sep;15(9):910-5. PMID:19172743
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (3deg.pdb1.gz) 234 Kb
  • LPC: Ligand-Protein Contacts for 3DEG
  • CSU: Contacts of Structural Units for 3DEG
  • Likely Quarternary Molecular Structure file(s) for 3DEG
  • Retrieve 3DEG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DEG from S2C, [Save to disk]
  • View 3DEG 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 3DEG
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3DEG, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3deg_C] [3deg_G] [3deg_B] [3deg_K] [3deg_H] [3deg_D] [3deg_J] [3deg_E] [3deg_I] [3deg_A] [3deg_F] [3deg]
  • SWISS-PROT database: [P60785] [P0A7J7] [P0A7S3]
  • Domain organization of [LEPA_ECOLI] [RL11_ECOLI] [RS12_ECOLI] by SWISSPFAM
  • Domains found in 3DEG: [EFG_C] [RL11 ] by SMART
  • Other resources with information on 3DEG
  • Community annotation for 3DEG 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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