4B3S Ribosome date Jul 26, 2012
title Crystal Structure Of The 30s Ribosome In Complex With Compou
authors C.L.Ng, K.Lang, D.Shcherbakov, T.Matt, D.Perez-Fernandez, R.Patak S.Duscha, R.Akbergenov, H.Boukari, P.Freihofer, I.Kudyba, M.S.K. R.S.Nandurikar, V.Ramakrishnan, A.Vasella, E.C.Bottger
compound source
Molecule: 16s Ribosomal Rna
Chain: A
 Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S2
Chain: B
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S19
Chain: S
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein Thx
Chain: V
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 5'-R(Upupcpapapap)-3'
Chain: W
Synonym: Mrna
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 5'-R(Gpgpgpapupupgpapapapapupcpcpc
Chain: Z
Synonym: Anticodon Stem Loop Asl
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852
symmetry Space Group: P 41 21 2
R_factor 0.210 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.150 401.150 173.640 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.15 Å
ligand K, MG, RPO, 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 reference4'-O-substitutions determine selectivity of aminoglycoside antibiotics., Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC, Nat Commun. 2014 Jan 28;5:3112. doi: 10.1038/ncomms4112. PMID:24473108
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1017 Kb) [Save to disk]
  • Biological Unit Coordinates (4b3s.pdb1.gz) 1002 Kb
  • LPC: Ligand-Protein Contacts for 4B3S
  • CSU: Contacts of Structural Units for 4B3S
  • Structure Factors (2097 Kb)
  • Retrieve 4B3S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B3S from S2C, [Save to disk]
  • Re-refined 4b3s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4B3S 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 4B3S
  • 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 4B3S, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b3s_R] [4b3s_L] [4b3s] [4b3s_G] [4b3s_C] [4b3s_H] [4b3s_W] [4b3s_T] [4b3s_I] [4b3s_V] [4b3s_Q] [4b3s_E] [4b3s_A] [4b3s_S] [4b3s_O] [4b3s_P] [4b3s_B] [4b3s_Z] [4b3s_K] [4b3s_D] [4b3s_J] [4b3s_F] [4b3s_M] [4b3s_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4B3S: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4B3S
  • Community annotation for 4B3S at PDBWiki (http://pdbwiki.org)

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