POP-OUT | CLOSE
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
2J00
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
2J00   2J01   2J02   2J03  
  Download All Files   

The complete entry has been assigned PDB ID 4V51 and is available for download in PDBx/mmCIF and PDBML/XML formats from the FTP archive at:
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v51.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v51.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 884072.97
    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 TT_C1100
    UniProtKB:   Protein Feature View | Search PDB | P62669  
    Molecule: 30S RIBOSOMAL PROTEIN S10
    Polymer: 10 Type: protein Length: 105
    Chains: J
    Organism Thermus thermophilus HB8
    Gene Names rpsJ rps10
    UniProtKB:   Protein Feature View | Search PDB | P80375  
    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 rps12
    UniProtKB:   Protein Feature View | Search PDB | P17293  
    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 rps14 rpsN
    UniProtKB:   Protein Feature View | Search PDB | P24320  
    Molecule: 30S RIBOSOMAL PROTEIN S15
    Polymer: 15 Type: protein Length: 89
    Chains: O
    Organism Thermus thermophilus HB8
    Gene Names rpsO rps15
    UniProtKB:   Protein Feature View | Search PDB | P80378  
    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 rps19
    UniProtKB:   Protein Feature View | Search PDB | P80381  
    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 Name rpsU
    UniProtKB:   Protein Feature View | Search PDB | P62612  
    Molecule: P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54)
    Polymer: 22 Type: rna Length: 77
    Chains: V
    Organism Escherichia coli K-12
    Molecule: E-SITE TRNA PHE OR A-SITE TRNA PHE (UNMODIFIED BASES)
    Polymer: 23 Type: rna Length: 76
    Chains: W, Y
    Organism Escherichia coli K-12
    Molecule: MRNA
    Polymer: 24 Type: rna Length: 24
    Chains: X
     
  •   Structure Validation Hide

    Download full validation report    

     
  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   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: Escherichia coli   Taxonomy    
    Polymer: 23
    Scientific Name: Escherichia coli   Taxonomy    
    Polymer: 24
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier 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
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    5MU
    Search 
    5MU C10 H15 N2 O9 P U rnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: 2J00
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (2J00 and 2J01)