3T1Y Ribosome Antibiotic date Jul 22, 2011
title Structure Of The Thermus Thermophilus 30s Ribosomal Subunit With A Human Anti-Codon Stem Loop (Hasl) Of Transfer Rna Ly (Trnalys3) Bound To An Mrna With An Aag-Codon In The A-Site Paromomycin
authors F.V.Murphy, F.A.P.Vendeix, W.Cantara, G.Leszczynska, E.M.Gustilo B.Sproat, A.A.P.Malkiewicz, P.F.Agris
compound source
Molecule: 16s Rrna
Chain: A
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 30s Ribosomal Protein S2
Chain: B
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

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: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039

Molecule: 30s Ribosomal Protein Thx
Chain: V
Synonym: S31
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Mrna A-Site Fragment
Chain: W
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Rna, As Naturally Occurring

Molecule: Trna Asl Human Lys3
Chain: X
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Rna, As Naturally Occurring
symmetry Space Group: P 41 21 2
R_factor 0.245 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
400.972 400.972 174.647 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 12A, 70U, MG, PAR, PSU, 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 referenceHuman tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism., Vendeix FA, Murphy FV 4th, Cantara WA, Leszczynska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF, J Mol Biol. 2011 Dec 29. PMID:22227389
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (941 Kb) [Save to disk]
  • Biological Unit Coordinates (3t1y.pdb1.gz) 927 Kb
  • LPC: Ligand-Protein Contacts for 3T1Y
  • CSU: Contacts of Structural Units for 3T1Y
  • Structure Factors (3078 Kb)
  • Retrieve 3T1Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3T1Y from S2C, [Save to disk]
  • Re-refined 3t1y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3T1Y 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 3T1Y
  • 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 3T1Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3t1y_E] [3t1y_J] [3t1y] [3t1y_V] [3t1y_N] [3t1y_D] [3t1y_C] [3t1y_Q] [3t1y_L] [3t1y_G] [3t1y_O] [3t1y_K] [3t1y_P] [3t1y_M] [3t1y_F] [3t1y_B] [3t1y_W] [3t1y_A] [3t1y_R] [3t1y_I] [3t1y_H] [3t1y_T] [3t1y_S] [3t1y_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3T1Y: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 3T1Y
  • Community annotation for 3T1Y at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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