THE CRYSTAL STRUCTURE OF EF-TU AND TRP-TRNA-TRP BOUND TO A COGNATE CODON ON THE 70S RIBOSOME.
DOI:10.2210/pdb2y19/pdb   NDB ID: 2Y19
2Y19
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
2Y10    2Y11    2Y18    2Y19   
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The complete entry has been assigned PDB ID 4V5R 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/4v5r.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v5r.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1421165.03
    Molecule: 50S RIBOSOMAL PROTEIN L27
    Polymer: 1 Type: protein Length: 85
    Chains: 0
    Organism: Thermus thermophilus HB8
    Gene Names: rpmA TTHA1782
    UniProtKB: Protein Feature View | Search PDB | P60493  
    Molecule: 50S RIBOSOMAL PROTEIN L28
    Polymer: 2 Type: protein Length: 98
    Chains: 1
    Organism: Thermus thermophilus HB8
    Gene Names: rpmB TTHA0042
    UniProtKB: Protein Feature View | Search PDB | P60494  
    Molecule: 50S RIBOSOMAL PROTEIN L29
    Polymer: 3 Type: protein Length: 72
    Chains: 2
    Organism: Thermus thermophilus HB8
    Gene Names: rpmC TTHA1684
    UniProtKB: Protein Feature View | Search PDB | Q5SHP6  
    Molecule: 50S RIBOSOMAL PROTEIN L30
    Polymer: 4 Type: protein Length: 60
    Chains: 3
    Organism: Thermus thermophilus HB8
    Gene Names: rpmD TTHA1674
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ6  
    Molecule: 50S RIBOSOMAL PROTEIN L31
    Polymer: 5 Type: protein Length: 71
    Chains: 4
    Organism: Thermus thermophilus HB8
    Gene Names: rpmE TTHA1073
    UniProtKB: Protein Feature View | Search PDB | Q5SJE1  
    Molecule: 50S RIBOSOMAL PROTEIN L32
    Polymer: 6 Type: protein Length: 60
    Chains: 5
    Organism: Thermus thermophilus HB8
    Gene Names: rpmF rpl32 TTHA0418
    UniProtKB: Protein Feature View | Search PDB | P80339  
    Molecule: 50S RIBOSOMAL PROTEIN L33
    Polymer: 7 Type: protein Length: 54
    Chains: 6
    Organism: Thermus thermophilus HB8
    Gene Names: rpmG rpl33 TTHA0250
    UniProtKB: Protein Feature View | Search PDB | P35871  
    Molecule: 50S RIBOSOMAL PROTEIN L34
    Polymer: 8 Type: protein Length: 49
    Chains: 7
    Organism: Thermus thermophilus HB8
    Gene Names: rpmH rpl34 TTHA0446
    UniProtKB: Protein Feature View | Search PDB | P80340  
    Molecule: 50S RIBOSOMAL PROTEIN L35
    Polymer: 9 Type: protein Length: 65
    Chains: 8
    Organism: Thermus thermophilus HB8
    Gene Names: rpmI TTHA0552
    UniProtKB: Protein Feature View | Search PDB | Q5SKU1  
    Molecule: 50S RIBOSOMAL PROTEIN L36
    Polymer: 10 Type: protein Length: 37
    Chains: 9
    Organism: Thermus thermophilus HB8
    Gene Names: rpmJ TTHA1668
    UniProtKB: Protein Feature View | Search PDB | Q5SHR2  
    Molecule: 23S RIBOSOMAL RNA
    Polymer: 11 Type: rna Length: 2915
    Chains: A
    Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
    Organism: Thermus thermophilus HB8
    Molecule: 5S RIBOSOMAL RNA
    Polymer: 12 Type: rna Length: 122
    Chains: B
    Organism: Thermus thermophilus HB8
    Molecule: 50S RIBOSOMAL PROTEIN L1
    Polymer: 13 Type: protein Length: 229
    Chains: C
    Organism: Thermus thermophilus HB8
    Gene Names: rplA TTHA0246
    UniProtKB: Protein Feature View | Search PDB | Q5SLP7  
    Molecule: 50S RIBOSOMAL PROTEIN L2
    Polymer: 14 Type: protein Length: 276
    Chains: D
    Organism: Thermus thermophilus HB8
    Gene Names: rplB TTHA1689
    UniProtKB: Protein Feature View | Search PDB | P60405  
    Molecule: 50S RIBOSOMAL PROTEIN L3
    Polymer: 15 Type: protein Length: 206
    Chains: E
    Organism: Thermus thermophilus HB8
    Gene Names: rplC TTHA1692
    UniProtKB: Protein Feature View | Search PDB | Q5SHN8  
    Molecule: 50S RIBOSOMAL PROTEIN L4
    Polymer: 16 Type: protein Length: 210
    Chains: F
    Organism: Thermus thermophilus HB8
    Gene Names: rplD TTHA1691
    UniProtKB: Protein Feature View | Search PDB | Q5SHN9  
    Molecule: 50S RIBOSOMAL PROTEIN L5
    Polymer: 17 Type: protein Length: 182
    Chains: G
    Organism: Thermus thermophilus HB8
    Gene Names: rplE TTHA1680
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ0  
    Molecule: 50S RIBOSOMAL PROTEIN L6
    Polymer: 18 Type: protein Length: 180
    Chains: H
    Organism: Thermus thermophilus HB8
    Gene Names: rplF TTHA1677
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ3  
    Molecule: 50S RIBOSOMAL PROTEIN L10
    Polymer: 19 Type: protein Length: 173
    Chains: J
    Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA
    Organism: Thermus thermophilus HB8
    Molecule: 50S RIBOSOMAL PROTEIN L11
    Polymer: 20 Type: protein Length: 147
    Chains: K
    Details: BUILT AS POLY-ALA
    Organism: Thermus thermophilus HB8
    Molecule: 50S RIBOSOMAL PROTEIN L13
    Polymer: 21 Type: protein Length: 140
    Chains: N
    Organism: Thermus thermophilus HB8
    Gene Names: rplM TTHA1465
    UniProtKB: Protein Feature View | Search PDB | P60488  
    Molecule: 50S RIBOSOMAL PROTEIN L14
    Polymer: 22 Type: protein Length: 122
    Chains: O
    Organism: Thermus thermophilus HB8
    Gene Names: rplN TTHA1682
    UniProtKB: Protein Feature View | Search PDB | Q5SHP8  
    Molecule: 50S RIBOSOMAL PROTEIN L15
    Polymer: 23 Type: protein Length: 150
    Chains: P
    Organism: Thermus thermophilus HB8
    Gene Names: rplO TTHA1673
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ7  
    Molecule: 50S RIBOSOMAL PROTEIN L16
    Polymer: 24 Type: protein Length: 141
    Chains: Q
    Organism: Thermus thermophilus HB8
    Gene Names: rplP TTHA1685
    UniProtKB: Protein Feature View | Search PDB | P60489  
    Molecule: 50S RIBOSOMAL PROTEIN L17
    Polymer: 25 Type: protein Length: 118
    Chains: R
    Organism: Thermus thermophilus HB8
    Gene Names: rplQ rpl17 TTHA1663
    UniProtKB: Protein Feature View | Search PDB | Q9Z9H5  
    Molecule: 50S RIBOSOMAL PROTEIN L18
    Polymer: 26 Type: protein Length: 112
    Chains: S
    Organism: Thermus thermophilus HB8
    Gene Names: rplR TTHA1676
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ4  
    Molecule: 50S RIBOSOMAL PROTEIN L19
    Polymer: 27 Type: protein Length: 146
    Chains: T
    Organism: Thermus thermophilus HB8
    Gene Names: rplS TTHA1031
    UniProtKB: Protein Feature View | Search PDB | P60490  
    Molecule: 50S RIBOSOMAL PROTEIN L20
    Polymer: 28 Type: protein Length: 118
    Chains: U
    Organism: Thermus thermophilus HB8
    Gene Names: rplT TTHA0553
    UniProtKB: Protein Feature View | Search PDB | P60491  
    Molecule: 50S RIBOSOMAL PROTEIN L21
    Polymer: 29 Type: protein Length: 101
    Chains: V
    Organism: Thermus thermophilus HB8
    Gene Names: rplU TTHA1783
    UniProtKB: Protein Feature View | Search PDB | P60492  
    Molecule: 50S RIBOSOMAL PROTEIN L22
    Polymer: 30 Type: protein Length: 113
    Chains: W
    Organism: Thermus thermophilus HB8
    Gene Names: rplV TTHA1687
    UniProtKB: Protein Feature View | Search PDB | Q5SHP3  
    Molecule: 50S RIBOSOMAL PROTEIN L23
    Polymer: 31 Type: protein Length: 96
    Chains: X
    Organism: Thermus thermophilus HB8
    Gene Names: rplW TTHA1690
    UniProtKB: Protein Feature View | Search PDB | Q5SHP0  
    Molecule: 50S RIBOSOMAL PROTEIN L24
    Polymer: 32 Type: protein Length: 110
    Chains: Y
    Organism: Thermus thermophilus HB8
    Gene Names: rplX TTHA1681
    UniProtKB: Protein Feature View | Search PDB | Q5SHP9  
    Molecule: 50S RIBOSOMAL PROTEIN L25
    Polymer: 33 Type: protein Length: 206
    Chains: Z
    Organism: Thermus thermophilus HB8
    Gene Names: rplY rpl25 rptL5 TTHA1589
    UniProtKB: Protein Feature View | Search PDB | Q5SHZ1  
     
  •   Structure Validation Hide

    View the full validation report  

     

  • MolProbity Ramachandran Plot
     

  •   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: Thermus thermophilus   Taxonomy    
    Polymer: 23
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 24
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 25
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 26
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 27
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 28
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 29
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 30
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 31
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 32
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 33
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1GD8   THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMALPROTEIN. 
    1GIY   CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION. THISFILE, 1GIY, CONTAINS THE 50S RIBOSOME SUBUNIT. THE 30SRIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES ARE IN THEFILE 1GIX 
    1V8Q   CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L27 FROM THERMUSTHERMOPHILUS HB8 
    1WKI   SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN L16 FROM THERMUSTHERMOPHILUS HB8 
    1YL3   CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR ANDTRNAS. LARGE SUBUNIT. THE COORDINATES FOR THE SMALLSUBUNIT ARE IN THE PDB ENTRY 1YL4. 
    2B66   50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASEFACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOME. THISFILE CONTAINS THE 50S SUBUNIT FROM A CRYSTAL STRUCTURE OFRELEASE FACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOMEAND IS DESCRIBED IN REMARK 400 
    2B9N   50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASEFACTOR RF2, TRNAS AND MRNA BOUND TO THE RIBOSOME. THISFILE CONTAINS THE 50S SUBUNIT FROM A CRYSTAL STRUCTURE OFRELEASE FACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOMEAND IS DESCRIBED IN REMARK 400. 
    2B9P   50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF THERIBOSOME IN COMPLEX WITH TRNAS AND MRNA WITH A STOP CODONIN THE A-SITE. THIS FILE CONTAINS THE 50S SUBUNIT FROM ACRYSTAL STRUCTURE OF THE RIBOSOME IN COMPLEX WITH TRNASAND MRNA WITH A STOP CODON IN THE A-SITE AND IS DESCRIBEDIN REMARK 400. 
    2J01   STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FROM MOLECULE I. 
    2J03   STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 4 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FROM MOLECULE II. 
    2JL6   INSIGHTS INTO TRANSLATIONAL TERMINATION FROM THE STRUCTURE OF RF2 BOUND TO THE RIBOSOME (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT. 
    2JL8   INSIGHTS INTO TRANSLATIONAL TERMINATION FROM THE STRUCTURE OF RF2 BOUND TO THE RIBOSOME (PART 4 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT. 
    2V47   STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, ASL- PHE AND TRNA-FMET (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FOR MOLECULE 1. 
    2V49   STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, ASL- PHE AND TRNA-FMET (PART 4 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT OF MOLECULE 2. 
    2WDI   STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME IN COMPLEX WITH MRNA, PAROMOMYCIN, ACYLATED A-SITE TRNA, DEACYLATED P-SITE TRNA, AND E-SITE TRNA. THIS FILE CONTAINS THE 50S SUBUNIT FOR MOLECULE I. 
    2WDJ   STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME IN COMPLEX WITH MRNA, PAROMOMYCIN, ACYLATED A-SITE TRNA, DEACYLATED P-SITE TRNA, AND E-SITE TRNA. THIS FILE CONTAINS THE 50S SUBUNIT FOR MOLECULE II. 
    2WDL   STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME IN COMPLEX WITH MRNA, PAROMOMYCIN, ACYLATED A- AND P-SITE TRNAS, AND E-SITE TRNA. THIS FILE CONTAINS THE 50S SUBUNIT FOR MOLECULE I. 
    2WDN   STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME IN COMPLEX WITH MRNA, PAROMOMYCIN, ACYLATED A- AND P-SITE TRNAS, AND E-SITE TRNA. THIS FILE CONTAINS THE 50S SUBUNIT FOR MOLECULE II. 
    2WH2   INSIGHTS INTO TRANSLATIONAL TERMINATION FROM THE STRUCTURE OF RF2 BOUND TO THE RIBOSOME 
    2WH4   INSIGHTS INTO TRANSLATIONAL TERMINATION FROM THE STRUCTURE OF RF2 BOUND TO THE RIBOSOME 
    2WRO   THE CRYSTAL STRUCTURE OF THE 70S RIBOSOME BOUND TO EF-TU AND TRNA (PART 2 OF 4). 
    2WRR   THE CRYSTAL STRUCTURE OF THE 70S RIBOSOME BOUND TO EF-TU AND TRNA (PART 4 OF 4). 
    2X9S   STRUCTURE OF THE 70S RIBOSOME BOUND TO RELEASE FACTOR 2 AND A SUBSTRATE ANALOG PROVIDES INSIGHTS INTO CATALYSIS OF PEPTIDE RELEASE 
    2X9U   STRUCTURE OF THE 70S RIBOSOME BOUND TO RELEASE FACTOR 2 AND A SUBSTRATE ANALOG PROVIDES INSIGHTS INTO CATALYSIS OF PEPTIDE RELEASE 
    2XG0   STRUCTURE OF CYTOTOXIC DOMAIN OF COLICIN E3 BOUND TO THE 70S RIBOSOME (PART 2 OF 4) 
    2XG2   STRUCTURE OF CYTOTOXIC DOMAIN OF COLICIN E3 BOUND TO THE 70S RIBOSOME (PART 4 OF 4) 
    2XQE   THE STRUCTURE OF EF-TU AND AMINOACYL-TRNA BOUND TO THE 70S RIBOSOME WITH A GTP ANALOG 
    2XTG   TRNA TRANLOCATION ON THE 70S RIBOSOME: THE PRE- TRANSLOCATIONAL TRANSLOCATION INTERMEDIATE TI(PRE) 
    2XUX   TRNA TRANLOCATION ON THE 70S RIBOSOME: THE POST- TRANSLOCATIONAL TRANSLOCATION INTERMEDIATE TI(POST) 
    2Y0V   THE CRYSTAL STRUCTURE OF EF-TU AND A9C-TRNA-TRP BOUND TO A NEAR-COGNATE CODON ON THE 70S RIBOSOME 
    2Y0X   THE CRYSTAL STRUCTURE OF EF-TU AND A9C-TRNA-TRP BOUND TO A NEAR-COGNATE CODON ON THE 70S RIBOSOME 
    2Y0Z   THE CRYSTAL STRUCTURE OF EF-TU AND G24A-TRNA-TRP BOUND TO A NEAR-COGNATE CODON ON THE 70S RIBOSOME 
    2Y10   THE CRYSTAL STRUCTURE OF EF-TU AND TRP-TRNA-TRP BOUND TO A COGNATE CODON ON THE 70S RIBOSOME. 
    2Y11   THE CRYSTAL STRUCTURE OF EF-TU AND TRP-TRNA-TRP BOUND TO A COGNATE CODON ON THE 70S RIBOSOME. 
    2Y13   THE CRYSTAL STRUCTURE OF EF-TU AND G24A-TRNA-TRP BOUND TO A NEAR-COGNATE CODON ON THE 70S RIBOSOME 
    2Y15   THE CRYSTAL STRUCTURE OF EF-TU AND G24A-TRNA-TRP BOUND TO A COGNATE CODON ON THE 70S RIBOSOME. 
    2Y17   EF-TU COMPLEX 3 
    2Y18   THE CRYSTAL STRUCTURE OF EF-TU AND TRP-TRNA-TRP BOUND TO A COGNATE CODON ON THE 70S RIBOSOME. 
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    UNK
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    UNK C4 H9 N O2 lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:2Y19
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Composite of PDB entries (2Y10 and 2Y11)