2E5L Ribosome date Dec 21, 2006
title A Snapshot Of The 30s Ribosomal Subunit Capturing Mrna Via T Dalgarno Interaction
authors T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schl K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, S.Yokoyama, Riken Stru Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: 16s Ribosomal Rna
Chain: A
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 5'-R(Gpapapapgpa)-3'
Chain: 1, 2
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 30s Ribosomal Protein S2
Chain: B
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S6
Chain: F
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S14
Chain: N
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S19
Chain: S
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein Thx
Chain: V
Synonym: S31
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor 0.259 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
411.790 411.790 173.160 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


Primary referenceA snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction., Kaminishi T, Wilson DN, Takemoto C, Harms JM, Kawazoe M, Schluenzen F, Hanawa-Suetsugu K, Shirouzu M, Fucini P, Yokoyama S, Structure. 2007 Mar;15(3):289-97. PMID:17355865
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (929 Kb) [Save to disk]
  • Biological Unit Coordinates (2e5l.pdb1.gz) 921 Kb
  • LPC: Ligand-Protein Contacts for 2E5L
  • CSU: Contacts of Structural Units for 2E5L
  • Likely Quarternary Molecular Structure file(s) for 2E5L
  • Structure Factors (2109 Kb)
  • Retrieve 2E5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E5L from S2C, [Save to disk]
  • Re-refined 2e5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2E5L 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 2E5L
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2E5L, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e5l_E] [2e5l] [2e5l_A] [2e5l_K] [2e5l_T] [2e5l_2] [2e5l_1] [2e5l_C] [2e5l_L] [2e5l_Q] [2e5l_H] [2e5l_B] [2e5l_G] [2e5l_V] [2e5l_O] [2e5l_I] [2e5l_D] [2e5l_M] [2e5l_S] [2e5l_J] [2e5l_R] [2e5l_F] [2e5l_P] [2e5l_N]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P80380] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P80374] [Q5SIH3]
  • Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_THET8] by SWISSPFAM
  • Domains found in 2E5L: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 2E5L
  • Community annotation for 2E5L 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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