STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUU-CODON IN THE A-SITE AND PAROMOMYCIN. DOI:10.2210/pdb2uub/pdb   NDB ID: 2UUB

2UUB   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+S)   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: 798485.24 Molecule: 16S RRNA Polymer: 1 Type: rna Length: 1522 Chains: A Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY Organism Thermus thermophilus HB8 Molecule: 30S RIBOSOMAL PROTEIN S2 Polymer: 2 Type: protein Length: 256 Chains: B Organism Thermus thermophilus HB8 Gene Names rpsB rps2 TTHA0861 UniProtKB:   Protein Feature View | Search PDB | P80371     Molecule: 30S RIBOSOMAL PROTEIN S3 Polymer: 3 Type: protein Length: 239 Chains: C Organism Thermus thermophilus HB8 Gene Names rpsC rps3 TTHA1686 UniProtKB:   Protein Feature View | Search PDB | P80372     Molecule: 30S RIBOSOMAL PROTEIN S4 Polymer: 4 Type: protein Length: 209 Chains: D Organism Thermus thermophilus HB8 Gene Names rpsD rps4 TTHA1665 UniProtKB:   Protein Feature View | Search PDB | P80373     Molecule: 30S RIBOSOMAL PROTEIN S5 Polymer: 5 Type: protein Length: 162 Chains: E Organism Thermus thermophilus HB8 Gene Names rpsE TTHA1675 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ5     Molecule: 30S RIBOSOMAL PROTEIN S6 Polymer: 6 Type: protein Length: 101 Chains: F Organism Thermus thermophilus HB8 Gene Names rpsF TTHA0245 UniProtKB:   Protein Feature View | Search PDB | Q5SLP8     Molecule: 30S RIBOSOMAL PROTEIN S7 Polymer: 7 Type: protein Length: 156 Chains: G Organism Thermus thermophilus HB8 Gene Names rpsG rps7 TTHA1696 UniProtKB:   Protein Feature View | Search PDB | P17291     Molecule: 30S RIBOSOMAL PROTEIN S8 Polymer: 8 Type: protein Length: 138 Chains: H Organism Thermus thermophilus HB8 Gene Names rpsH TTHA1678 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ2     Molecule: 30S RIBOSOMAL PROTEIN S9 Polymer: 9 Type: protein Length: 128 Chains: I Organism Thermus thermophilus HB8 Gene Names rpsI rps9 TTHA1464 UniProtKB:   Protein Feature View | Search PDB | P80374     Molecule: 30S RIBOSOMAL PROTEIN S10 Polymer: 10 Type: protein Length: 105 Chains: J Organism Thermus thermophilus HB8 Gene Names rpsJ TTHA1693 UniProtKB:   Protein Feature View | Search PDB | Q5SHN7     Molecule: 30S RIBOSOMAL PROTEIN S11 Polymer: 11 Type: protein Length: 129 Chains: K Organism Thermus thermophilus HB8 Gene Names rpsK rps11 TTHA1666 UniProtKB:   Protein Feature View | Search PDB | P80376     Molecule: 30S RIBOSOMAL PROTEIN S12 Polymer: 12 Type: protein Length: 135 Chains: L Organism Thermus thermophilus HB8 Gene Names rpsL TTHA1697 UniProtKB:   Protein Feature View | Search PDB | Q5SHN3     Molecule: 30S RIBOSOMAL PROTEIN S13 Polymer: 13 Type: protein Length: 126 Chains: M Organism Thermus thermophilus HB8 Gene Names rpsM rps13 TTHA1667 UniProtKB:   Protein Feature View | Search PDB | P80377     Molecule: 30S RIBOSOMAL PROTEIN S14 Polymer: 14 Type: protein Length: 61 Chains: N Organism Thermus thermophilus HB8 Gene Names rpsZ rpsN TTHA1679 UniProtKB:   Protein Feature View | Search PDB | Q5SHQ1     Molecule: 30S RIBOSOMAL PROTEIN S15 Polymer: 15 Type: protein Length: 89 Chains: O Organism Thermus thermophilus HB8 Gene Names rpsO TTHA1138 UniProtKB:   Protein Feature View | Search PDB | Q5SJ76     Molecule: 30S RIBOSOMAL PROTEIN S16 Polymer: 16 Type: protein Length: 88 Chains: P Organism Thermus thermophilus HB8 Gene Names rpsP TTHA1035 UniProtKB:   Protein Feature View | Search PDB | Q5SJH3     Molecule: 30S RIBOSOMAL PROTEIN S17 Polymer: 17 Type: protein Length: 105 Chains: Q Organism Thermus thermophilus HB8 Gene Names rpsQ TTHA1683 UniProtKB:   Protein Feature View | Search PDB | Q5SHP7     Molecule: 30S RIBOSOMAL PROTEIN S18 Polymer: 18 Type: protein Length: 88 Chains: R Organism Thermus thermophilus HB8 Gene Names rpsR TTHA0243 UniProtKB:   Protein Feature View | Search PDB | Q5SLQ0     Molecule: 30S RIBOSOMAL PROTEIN S19 Polymer: 19 Type: protein Length: 93 Chains: S Organism Thermus thermophilus HB8 Gene Names rpsS TTHA1688 UniProtKB:   Protein Feature View | Search PDB | Q5SHP2     Molecule: 30S RIBOSOMAL PROTEIN S20 Polymer: 20 Type: protein Length: 106 Chains: T Organism Thermus thermophilus HB8 Gene Names rpsT rps20 TTHA1397 UniProtKB:   Protein Feature View | Search PDB | P80380     Molecule: 30S RIBOSOMAL PROTEIN THX Polymer: 21 Type: protein Length: 27 Chains: U Organism Thermus thermophilus HB8 Gene Names rpsU TTHA1396 UniProtKB:   Protein Feature View | Search PDB | Q5SIH3     Molecule: 5'-R(*GP*UP*UP*AP*AP*AP)-3' Polymer: 22 Type: rna Length: 6 Chains: X Molecule: 5'-R(*CP*CP*UP*CP*CP*CP*UP*CM0P*AP*CP*6MZP*AP *GP*GP*AP*GP*G)-3' Polymer: 23 Type: rna Length: 17 Chains: Y     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: Synthetic construct   Taxonomy     Polymer: 23 Scientific Name: Synthetic construct   Taxonomy         Related PDB Entries Hide Identifier Details 1DV4  PARTIAL STRUCTURE OF 16S RIBONUCLEIC ACID OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS  1EG0  FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E .COLI 70S RIBOSOME  1EMI  STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMALPROTEIN S8.  1FJG  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH THE ANTIBIOTICS STREPTOMYCIN, SPECTINOMYCIN,AND PAROMOMYCIN  1FKA  STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNITAT 3.3 A RESOLUTION  1G1X  STRUCTURE OF RIBOSOMAL PROTEINS S15, S6, S18 , AND 16SRIBOSOMAL RNA  1GIX  CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION. THISFILE, 1GIX, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA,AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY  1HNW  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH TETRACYCLINE  1HNX  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH PACTAMYCIN  1HNZ  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH HYGROMYCIN B  1HR0  CRYSTAL STRUCTURE OF INITIATION FACTOR IF1 BOUND TO THE 30SRIBOSOMAL SUBUNIT  1I94  CRYSTAL STRUCTURES OF THE SMALL RIBOSOMAL SUBUNIT WITHTETRACYCLINE, EDEINE AND IF3  1I95  CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUSTHERMOPHILUS IN COMPLEX WITH EDEINE  1I96  CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUSTHERMOPHILUS IN COMPLEX WITH THE TRANSLATION INITIATIONFACTOR IF3 (C- TERMINAL DOMAIN)  1I97  CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUSTHERMOPHILUS IN COMPLEX WITH TETRACYCLINE  1IBK  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN  1IBL  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATETRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE ANDWITH THE ANTIBIOTIC PAROMOMYCIN  1IBM  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATETRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE  1J5E  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT  1JGO  THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE,1JGO, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, ANDMRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY  1JGP  THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE,1JGP, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, ANDMRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY  1JGQ  THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE,1JGQ, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, ANDMRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY  1L1U  TERNARY COMPLEX DOCKED IN THE DECODING SITE OF THE 30SRIBOSOMAL SUBUNIT  1MVR  DECODING CENTER & PEPTIDYL TRANSFERASE CENTER FROM THE X-RAY STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME,ALIGNED TO THE LOW RESOLUTION CRYO-EM MAP OF E.COLI 70SRIBOSOME  1N32  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITBOUND TO CODON AND NEAR- COGNATE TRANSFER RNA ANTICODONSTEM-LOOP MISMATCHED AT THE FIRST CODON POSITION AT THE ASITE WITH PAROMOMYCIN  1N33  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITBOUND TO CODON AND NEAR- COGNATE TRANSFER RNA ANTICODONSTEM-LOOP MISMATCHED AT THE SECOND CODON POSITION AT THE ASITE WITH PAROMOMYCIN  1N34  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN THE PRESENCE OF CODON AND CRYSTALLOGRAPHICALLYDISORDERED NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOPMISMATCHED AT THE FIRST CODON POSITION  1N36  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN THE PRESENCE OF CRYSTALLOGRAPHICALLY DISORDERED CODONAND NEAR- COGNATE TRANSFER RNA ANTICODON STEM- LOOPMISMATCHED AT THE SECOND CODON POSITION  1PN7  COORDINATES OF S12, L11 PROTEINS AND P- TRNA, FROM THE 70S X-RAY STRUCTURE ALIGNED TO THE 70S CRYO-EM MAP OF E. COLIRIBOSOME  1PN8  COORDINATES OF S12, L11 PROTEINS AND E- SITE TRNA FROM 70SCRYSTAL STRUCTURE SEPARATELY FITTED INTO THE CRYO-EM MAPOF E.COLI 70S.EF-G.GDPNP COMPLEX. THE ATOMIC COORDINATESORIGINALLY FROM THE E-SITE TRNA WERE FITTED IN THEPOSITION OF THE HYBRID P /E-SITE TRNA.  1PNS  CRYSTAL STRUCTURE OF A STREPTOMYCIN DEPENDENT RIBOSOME FROME. COLI, 30S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1PNS,CONTAINS THE 30S SUBUNIT, TWO TRNAS, AND ONE MRNAMOLECULE. THE 50S RIBOSOMAL SUBUNIT IS IN FILE 1PNU.  1PNX  CRYSTAL STRUCTURE OF THE WILD TYPE RIBOSOME FROM E. COLI,30S SUBUNIT OF 70S RIBOSOME . THIS FILE, 1PNX, CONTAINSONLY MOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50SSUBUNIT IS IN THE PDB FILE 1PNY.  1QD7  PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT  1QZC  COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTEDINTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX(GDP.KIRROMYCIN) BOUND 70S RIBOSOME  1RSS  RIBOSOMAL PROTEIN S7 FROM THERMUS THERMOPHILUS  1TWT  MODEL STRUCTURE OF THE T. THERMOPHILUS 70S RIBOSOME, 30SSUBUNIT OF 70S ROBOSOME. THIS FILE, 1TWT, CONTAINS ONLYMOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50S SUBUNIT ISIN THE PDB FILE 1TWV.  1XMO  CRYSTAL STRUCTURE OF MNM5U34T6A37-TRNALYSUUU COMPLEXED WITHAAG-MRNA IN THE DECODING CENTER  1XMQ  CRYSTAL STRUCTURE OF T6A37-ASLLYSUUU AAA- MRNA BOUND TO THEDECODING CENTER  1XNQ  STRUCTURE OF AN INOSINE-ADENINE WOBBLE BASE PAIR COMPLEX INTHE CONTEXT OF THE DECODING CENTER  1XNR  CRYSTAL STRUCTURE OF AN INOSINE-CYTOSINE WOBBLE BASE PAIRIN THE CONTEXT OF THE DECODING CENTER  1YL4  CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR ANDTRNAS. 30S SUBUNIT. THE COORDINATES FOR THE 50S SUBUNITARE IN THE PDB ENTRY 1YL3  2B64  30S RIBOSOMAL SUBUNIT, TRNAS, MRNA AND RELEASE FACTOR RF1FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX.THIS FILE CONTAINS THE 30S SUBUNIT, TRNAS, MRNA ANDRELEASE FACTOR RF1 FROM A CRYSTAL STRUCTURE OF THE WHOLERIBOSOMAL COMPLEX". THE ENTIRE CRYSTAL STRUCTURE CONTAINSONE 70S RIBOSOME, TRNAS, MRNA AND RELEASE FACTOR RF1 ANDIS DESCRIBED IN REMARK 400.  2B9M  30S RIBOSOMAL SUBUNIT, TRNAS, MRNA AND RELEASE FACTOR RF2FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX.THIS FILE CONTAINS THE 30S RIBOSOMAL SUBUNIT, TRNAS, MRNAAND RELEASE FACTOR RF2 FROM A CRYSTAL STRUCTURE OF THEWHOLE RIBOSOMAL COMPLEX". THE ENTIRE CRYSTAL STRUCTURECONTAINS ONE 70S RIBOSOME, TRNAS, MRNA AND RELEASE FACTORRF2 AND IS DESCRIBED IN REMARK 400.  2B9O  30S RIBOSOMAL SUBUNIT, TRNAS AND MRNA FROM A CRYSTALSTRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX WITH A STOP CODONIN THE A-SITE. THIS FILE CONTAINS THE 30S SUBUNIT, TRNASAND MRNA FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMALCOMPLEX WITH A STOP CODON IN THE A-SITE AND IS DESCRIBEDIN REMARK 400.  2F4V  30S RIBOSOME + DESIGNER ANTIBIOTIC  2J00  STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN  2J02  STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN  2UU9  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUG-CODON IN THE A-SITE AND PAROMOMYCIN.  2UUA  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUC-CODON IN THE A-SITE AND PAROMOMYCIN.  2UUC  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUA-CODON IN THE A-SITE AND PAROMOMYCIN.      Ligand Chemical Component Hide Identifier Formula Name Interactions K Search  Download  K POTASSIUM ION   Ligand Explorer 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 CM0 Search  C11 H15 N2 O12 P rnaLinking 6MZ Search  C11 H16 N5 O7 P A rnaLinking     External Domain Annotations Hide SCOP Classification v1.75: 21 Domains - data from SCOP   CATH Classification v3.4.0: 22 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: 2UUB     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PQS (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Weixlbaumer, A.,  Murphy, F.V.,  Dziergowska, A.,  Malkiewicz, A.,  Vendeix, F.A.P.,  Agris, P.F.,  Ramakrishnan, V. Deposition:   2007-03-01 Release:   2007-05-15 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 Resolution[Å]:   2.80 R-Value: 0.219 (obs.) R-Free: 0.243 Space Group: P 41 21 2 Unit Cell:   Length [Å] Angles [°] a = 400.44 α = 90.00  b = 400.44 β = 90.00  c = 173.36 γ = 90.00      Molecule of the Month Hide Ribosomal Subunits Ribosome Aminoglycoside Antibiotics Transfer-Messenger RNA