1N33 Ribosome date Oct 25, 2002
title Structure Of The Thermus Thermophilus 30s Ribosomal Subunit Bound To Codon And Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched At The Second Codon Position At The A Site With Paromomycin
authors J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan
compound source
Molecule: 16s Ribosomal Rna
Chain: A
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Anticodon Stem-Loop Of Ser Transfer Rna
Chain: Y
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: A-Site Messenger Rna Fragment
Chain: Z
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

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
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor 0.225 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.599 401.599 176.025 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.35 Å
ligand 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 referenceSelection of tRNA by the ribosome requires a transition from an open to a closed form., Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V, Cell 2002 Nov 27;111(5):721-32. PMID:12464183
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (967 Kb) [Save to disk]
  • Biological Unit Coordinates (1n33.pdb1.gz) 947 Kb
  • LPC: Ligand-Protein Contacts for 1N33
  • CSU: Contacts of Structural Units for 1N33
  • Likely Quarternary Molecular Structure file(s) for 1N33
  • Structure Factors (1632 Kb)
  • Retrieve 1N33 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N33 from S2C, [Save to disk]
  • Re-refined 1n33 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1N33 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 1N33
  • 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 1N33, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n33b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1n33c2, region C:107-207 [Jmol] [rasmolscript] [script source]
        - Domain d1n33c1, region C:2-106 [Jmol] [rasmolscript] [script source]
        - Domain d1n33d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1n33e2, region E:5-73 [Jmol] [rasmolscript] [script source]
        - Domain d1n33e1, region E:74-154 [Jmol] [rasmolscript] [script source]
        - Domain d1n33f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1n33g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1n33h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1n33i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1n33j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1n33k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1n33l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1n33m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1n33n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1n33o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1n33p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1n33q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1n33r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1n33s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1n33t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1n33v_, region V [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n33_I] [1n33_C] [1n33_H] [1n33_D] [1n33_P] [1n33_F] [1n33_B] [1n33_A] [1n33_O] [1n33] [1n33_G] [1n33_Z] [1n33_Y] [1n33_V] [1n33_Q] [1n33_T] [1n33_J] [1n33_M] [1n33_S] [1n33_R] [1n33_L] [1n33_E] [1n33_N] [1n33_K]
  • 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 1N33: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 1N33
  • Community annotation for 1N33 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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