STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 1 OF 4). THIS FILE CONTAINS THE 30S SUBUNIT, MRNA, A-, P- AND E-SITE TRNAS AND PAROMOMYCIN FOR MOLECULE I.     DOI:10.2210/pdb2j00/pdb   NDB ID: 2J00

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Split Entry The asymmetric unit for this structure is composed of multiple PDB entries: 2J00   2J01   2J02   2J03   Download All Files          Primary Citation       Molecular Description Hide Classification: Ribosome Structure Weight: 884072.97   Molecule: 16S RRNA Polymer: 1 Type: polyribonucleotide Length: 1522 Chains: A Other Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY. Molecule: 30S RIBOSOMAL PROTEIN S2 Polymer: 2 Type: polypeptide(L) Length: 256 Chains: B Molecule: 30S RIBOSOMAL PROTEIN S3 Polymer: 3 Type: polypeptide(L) Length: 239 Chains: C Molecule: 30S RIBOSOMAL PROTEIN S4 Polymer: 4 Type: polypeptide(L) Length: 209 Chains: D Molecule: 30S RIBOSOMAL PROTEIN S5 Polymer: 5 Type: polypeptide(L) Length: 162 Chains: E Molecule: 30S RIBOSOMAL PROTEIN S6 Polymer: 6 Type: polypeptide(L) Length: 101 Chains: F Molecule: 30S RIBOSOMAL PROTEIN S7 Polymer: 7 Type: polypeptide(L) Length: 156 Chains: G Molecule: 30S RIBOSOMAL PROTEIN S8 Polymer: 8 Type: polypeptide(L) Length: 138 Chains: H Molecule: 30S RIBOSOMAL PROTEIN S9 Polymer: 9 Type: polypeptide(L) Length: 128 Chains: I Molecule: 30S RIBOSOMAL PROTEIN S10 Polymer: 10 Type: polypeptide(L) Length: 105 Chains: J Molecule: 30S RIBOSOMAL PROTEIN S11 Polymer: 11 Type: polypeptide(L) Length: 129 Chains: K Molecule: 30S RIBOSOMAL PROTEIN S12 Polymer: 12 Type: polypeptide(L) Length: 135 Chains: L Molecule: 30S RIBOSOMAL PROTEIN S13 Polymer: 13 Type: polypeptide(L) Length: 126 Chains: M Molecule: 30S RIBOSOMAL PROTEIN S14 Polymer: 14 Type: polypeptide(L) Length: 61 Chains: N Molecule: 30S RIBOSOMAL PROTEIN S15 Polymer: 15 Type: polypeptide(L) Length: 89 Chains: O Molecule: 30S RIBOSOMAL PROTEIN S16 Polymer: 16 Type: polypeptide(L) Length: 88 Chains: P Molecule: 30S RIBOSOMAL PROTEIN S17 Polymer: 17 Type: polypeptide(L) Length: 105 Chains: Q Molecule: 30S RIBOSOMAL PROTEIN S18 Polymer: 18 Type: polypeptide(L) Length: 88 Chains: R Molecule: 30S RIBOSOMAL PROTEIN S19 Polymer: 19 Type: polypeptide(L) Length: 93 Chains: S Molecule: 30S RIBOSOMAL PROTEIN S20 Polymer: 20 Type: polypeptide(L) Length: 106 Chains: T Molecule: 30S RIBOSOMAL PROTEIN THX Polymer: 21 Type: polypeptide(L) Length: 27 Chains: U Molecule: P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54) Polymer: 22 Type: polyribonucleotide Length: 77 Chains: V Molecule: E-SITE TRNA PHE OR A-SITE TRNA PHE (UNMODIFIED BASES) Polymer: 23 Type: polyribonucleotide Length: 76 Chains: W, Y Molecule: MRNA Polymer: 24 Type: polyribonucleotide Length: 24 Chains: X       Source Hide Polymer: 1 Scientific Name: Thermus thermophilus   Polymer: 2 Scientific Name: Thermus thermophilus   Polymer: 3 Scientific Name: Thermus thermophilus   Polymer: 4 Scientific Name: Thermus thermophilus   Polymer: 5 Scientific Name: Thermus thermophilus   Polymer: 6 Scientific Name: Thermus thermophilus   Polymer: 7 Scientific Name: Thermus thermophilus   Polymer: 8 Scientific Name: Thermus thermophilus   Polymer: 9 Scientific Name: Thermus thermophilus   Polymer: 10 Scientific Name: Thermus thermophilus   Polymer: 11 Scientific Name: Thermus thermophilus   Polymer: 12 Scientific Name: Thermus thermophilus   Polymer: 13 Scientific Name: Thermus thermophilus   Polymer: 14 Scientific Name: Thermus thermophilus   Polymer: 15 Scientific Name: Thermus thermophilus   Polymer: 16 Scientific Name: Thermus thermophilus   Polymer: 17 Scientific Name: Thermus thermophilus   Polymer: 18 Scientific Name: Thermus thermophilus   Polymer: 19 Scientific Name: Thermus thermophilus   Polymer: 20 Scientific Name: Thermus thermophilus   Polymer: 21 Scientific Name: Thermus thermophilus   Polymer: 22 Scientific Name: Escherichia coli   Polymer: 23 Scientific Name: Escherichia coli   Polymer: 24 Scientific Name: Synthetic construct         Related PDB Entries Hide Id Details 1FJG  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH THE ANTIBIOTICS STREPTOMYCIN, SPECTINOMYCIN,AND PAROMOMYCIN  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  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  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  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.  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  2J01  STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 2 OF 4)  2J02  STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 3 OF 4)  2J03  STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 4 OF 4)        Ligand Chemical Component Hide Identifier Name Formula Interaction View Links MG     MAGNESIUM ION Mg Ligand Explorer PAR     PAROMOMYCIN C23 H45 N5 O14 Ligand Explorer ZN     ZINC ION Zn Ligand Explorer       Modified Residues Hide Identifier Name Formula Interaction View Links 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE (parent: U)(type: rnaLinking) C10 H15 N2 O9 P Ligand Explorer       Derived Data Hide SCOP Classification v1.75 - (22 Domains) CATH Classification v3.2.0 - (18 Domains) PFAM Classification - (23 Domains) GO Terms - (152 Terms)     Reset Layout

Biological Assembly 1     More Images... View in Jmol Composite of PDB entries (2J00 and 2J01)         Deposition Summary Hide Authors:   Selmer, M.,   Dunham, C.M.,   Murphy, F.V.,   Weixlbaumer, A.,   Petry, S.,   Weir, J.R.,   Kelley, A.C.,   Ramakrishnan, V. Deposition:   2006-07-31 Release:   2006-09-28 Last Modified (REVDAT):   2009-02-24       Experimental Details Hide Method:   X-RAY DIFFRACTION Experimental Data:   Resolution[Å]: 2.80 R-Value: 0.271 (obs.) R-Free: 0.313 Space Group: P 21 21 21 Unit Cell:   Length [Å] Angles [°] a = 213.32 α = 90.00  b = 452.95 β = 90.00  c = 631.36 γ = 90.00        Structure Links Hide Molecule of the Month Features: Ribosome 70S Ribosomes