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 DOI:10.2210/pdb1n33/pdb   NDB ID: RR0057

1N33   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Ribosome Structure Weight: 793101.68 Molecule: 16S RIBOSOMAL RNA Polymer: 1 Type: rna Length: 1522 Chains: A Organism Thermus thermophilus Molecule: ANTICODON STEM-LOOP OF SER TRANSFER RNA Polymer: 2 Type: rna Length: 17 Chains: Y Organism Thermus thermophilus Molecule: A-SITE MESSENGER RNA FRAGMENT Polymer: 3 Type: rna Length: 6 Chains: Z Organism Thermus thermophilus Molecule: 30S RIBOSOMAL PROTEIN S2 Polymer: 4 Type: protein Length: 256 Chains: B Organism Thermus thermophilus Gene Names rpsB rps2 TTHA0861 UniProtKB:   Protein Feature View | Search PDB | P80371     Molecule: 30S RIBOSOMAL PROTEIN S3 Polymer: 5 Type: protein Length: 239 Chains: C Organism Thermus thermophilus Gene Names rpsC rps3 TTHA1686 UniProtKB:   Protein Feature View | Search PDB | P80372     Molecule: 30S RIBOSOMAL PROTEIN S4 Polymer: 6 Type: protein Length: 208 Chains: D Organism Thermus thermophilus Gene Names rpsD rps4 TTHA1665 UniProtKB:   Protein Feature View | Search PDB | P80373     Molecule: 30S RIBOSOMAL PROTEIN S5 Polymer: 7 Type: protein Length: 161 Chains: E Organism Thermus thermophilus Gene Names rpsE TTHA1675 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ5     Molecule: 30S RIBOSOMAL PROTEIN S6 Polymer: 8 Type: protein Length: 101 Chains: F Organism Thermus thermophilus Gene Names rpsF TTHA0245 UniProtKB:   Protein Feature View | Search PDB | Q5SLP8     Molecule: 30S RIBOSOMAL PROTEIN S7 Polymer: 9 Type: protein Length: 155 Chains: G Organism Thermus thermophilus Gene Names rpsG rps7 TTHA1696 UniProtKB:   Protein Feature View | Search PDB | P17291     Molecule: 30S RIBOSOMAL PROTEIN S8 Polymer: 10 Type: protein Length: 138 Chains: H Organism Thermus thermophilus Gene Names rpsH TTHA1678 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ2     Molecule: 30S RIBOSOMAL PROTEIN S9 Polymer: 11 Type: protein Length: 128 Chains: I Organism Thermus thermophilus Gene Names rpsI rps9 TTHA1464 UniProtKB:   Protein Feature View | Search PDB | P80374     Molecule: 30S RIBOSOMAL PROTEIN S10 Polymer: 12 Type: protein Length: 104 Chains: J Organism Thermus thermophilus Gene Names rpsJ TTHA1693 UniProtKB:   Protein Feature View | Search PDB | Q5SHN7     Molecule: 30S RIBOSOMAL PROTEIN S11 Polymer: 13 Type: protein Length: 129 Chains: K Organism Thermus thermophilus Gene Names rpsK rps11 TTHA1666 UniProtKB:   Protein Feature View | Search PDB | P80376     Molecule: 30S RIBOSOMAL PROTEIN S12 Polymer: 14 Type: protein Length: 135 Chains: L Organism Thermus thermophilus Gene Names rpsL TTHA1697 UniProtKB:   Protein Feature View | Search PDB | Q5SHN3     Molecule: 30S RIBOSOMAL PROTEIN S13 Polymer: 15 Type: protein Length: 126 Chains: M Organism Thermus thermophilus Gene Names rpsM rps13 TTHA1667 UniProtKB:   Protein Feature View | Search PDB | P80377     Molecule: 30S RIBOSOMAL PROTEIN S14 Polymer: 16 Type: protein Length: 60 Chains: N Organism Thermus thermophilus Gene Names rpsZ rpsN TTHA1679 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ1     Molecule: 30S RIBOSOMAL PROTEIN S15 Polymer: 17 Type: protein Length: 88 Chains: O Organism Thermus thermophilus Gene Names rpsO TTHA1138 UniProtKB:   Protein Feature View | Search PDB | Q5SJ76     Molecule: 30S RIBOSOMAL PROTEIN S16 Polymer: 18 Type: protein Length: 88 Chains: P Organism Thermus thermophilus Gene Names rpsP TTHA1035 UniProtKB:   Protein Feature View | Search PDB | Q5SJH3     Molecule: 30S RIBOSOMAL PROTEIN S17 Polymer: 19 Type: protein Length: 104 Chains: Q Organism Thermus thermophilus Gene Names rpsQ TTHA1683 UniProtKB:   Protein Feature View | Search PDB | Q5SHP7     Molecule: 30S RIBOSOMAL PROTEIN S18 Polymer: 20 Type: protein Length: 88 Chains: R Organism Thermus thermophilus Gene Names rpsR TTHA0243 UniProtKB:   Protein Feature View | Search PDB | Q5SLQ0     Molecule: 30S RIBOSOMAL PROTEIN S19 Polymer: 21 Type: protein Length: 92 Chains: S Organism Thermus thermophilus Gene Names rpsS TTHA1688 UniProtKB:   Protein Feature View | Search PDB | Q5SHP2     Molecule: 30S RIBOSOMAL PROTEIN S20 Polymer: 22 Type: protein Length: 106 Chains: T Organism Thermus thermophilus Gene Names rpsT rps20 TTHA1397 UniProtKB:   Protein Feature View | Search PDB | P80380     Molecule: 30S RIBOSOMAL PROTEIN THX Polymer: 23 Type: protein Length: 26 Chains: V Organism Thermus thermophilus Gene Names rpsU TTHA1396 UniProtKB:   Protein Feature View | Search PDB | Q5SIH3         Source Hide Polymer: 1 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 2 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 3 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 4 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 5 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 6 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 7 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 8 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 9 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 10 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 11 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 12 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 13 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 14 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 15 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 16 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 17 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 18 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 19 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 20 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 21 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 22 Scientific Name: Thermus thermophilus   Taxonomy     Polymer: 23 Scientific Name: Thermus thermophilus   Taxonomy         Related PDB Entries Hide Identifier Details 1FJG  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH THE ANTIBIOTICS STREPTOMYCIN, SPECTINOMYCIN AND PAROMOMYCIN  1IBK  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH P-SITE MESSENGER RNA FRAGMENT AND WITH THE ANTIBIOTIC PAROMOMYCIN  1IBL  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND TO THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN  1IBM  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND TO THE A SITE  1J5E  NATIVE STRUCTURE OF THE 30S PARTICLE  1N32  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT BOUND TO CODON AND NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE FIRST CODON POSITION AT THE A SITE WITH PAROMOMYCIN  1N34  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN THE PRESENCE OF CODON AND CRYSTALLOGRAPHICALLY DISORDERED NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE FIRST CODON POSITION  1N36  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN THE PRESENCE OF CRYSTALLOGRAPHICALLY DISORDERED CODON AND NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE SECOND CODON POSITION      Ligand Chemical Component Hide Identifier Formula Name Interactions MG Search  Download  Mg MAGNESIUM ION   Ligand Explorer PAR Search  Download  C23 H45 N5 O14 PAROMOMYCIN   Ligand Explorer ZN Search  Download  Zn ZINC ION   Ligand Explorer     Modified Residues Hide Identifier Formula Parent Type PSU Search  C9 H13 N2 O9 P U rnaLinking     External Domain Annotations Hide SCOP Classification v1.75: 22 Domains - data from SCOP   CATH Classification v3.4.0: 23 Domains - data from CATH   Pfam Classification: 22 Domains - data from Pfam   GO Terms: 150 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: RR0057     Data in orange boxes are gathered from external resources (when available). Reset Layout

Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Ogle, J.M.,  Murphy IV, F.V.,  Tarry, M.J.,  Ramakrishnan, V. Deposition:   2002-10-25 Release:   2002-11-29 Last Modified (REVDAT):   2009-02-24     Revision History    Hide Mouse over text for details 2011-07-13 Version format compliance     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   3.35 R-Value: 0.225 (obs.) R-Free: 0.284 Space Group: P 41 21 2 Unit Cell:   Length [Å] Angles [°] a = 401.60 α = 90.00  b = 401.60 β = 90.00  c = 176.02 γ = 90.00      Molecule of the Month Hide Ribosomal Subunits Ribosome Aminoglycoside Antibiotics Transfer-Messenger RNA