4V5M

tRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit tRNA Hybrid Sites.

Ratje, A.H.Loerke, J.Mikolajka, A.Brunner, M.Hildebrand, P.W.Starosta, A.L.Donhofer, A.Connell, S.R.Fucini, P.Mielke, T.Whitford, P.C.Onuchic, J.N.Yu, Y.Sanbonmatsu, K.Y.Hartmann, R.K.Penczek, P.A.Wilson, D.N.Spahn, C.M.T.

(2010) Nature 468: 713

  • DOI: 10.1038/nature09547
  • Primary Citation of Related Structures:  
    4V5M, 4V5N

  • PubMed Abstract: 
  • The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen t ...

    The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P site) on the 30S head and simultaneously establishes interaction with the exit site (E site) on the 30S platform, a novel intra-subunit 'pe/E' hybrid state is formed. This state is stabilized by domain IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the 'missing link' in terms of tRNA intermediates involved in the universally conserved translocation process.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2AB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4AD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7AG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12AL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18AR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19AS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6BH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13BN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15BP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20BU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21BV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24BY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10AJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11AK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13AM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE ZAN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15AO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16AP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17AQ105Thermus thermophilus HB8Mutation(s): 0 
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20AT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXAU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGATION FACTOR GAY691Thermus thermophilus HB8Mutation(s): 0 
Gene Names: fusAfusTTHA1695
Find proteins for Q5SHN5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27B085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28B198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29B272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30B360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31B471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3AC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32B560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L33B654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L34B749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L35B865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 34
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50S RIBOSOMAL PROTEIN L36B937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1BC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 38
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50S RIBOSOMAL PROTEIN L2BD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 39
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50S RIBOSOMAL PROTEIN L3BE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 40
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50S RIBOSOMAL PROTEIN L4BF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L5BG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L11BK147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 44
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50S RIBOSOMAL PROTEIN L7/L12BL121Escherichia coli K-12Mutation(s): 0 
Gene Names: rplLb3986JW3949
Find proteins for P0A7K2 (Escherichia coli (strain K12))
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L14BO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L16BQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 49
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50S RIBOSOMAL PROTEIN L17BR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
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30S RIBOSOMAL PROTEIN S5AE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 50
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50S RIBOSOMAL PROTEIN L18BS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 51
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50S RIBOSOMAL PROTEIN L19BT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
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50S RIBOSOMAL PROTEIN L22BW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23BX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHP0
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25BZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHZ1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6AF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SLP8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8AH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9AI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  P80374
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAAA1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
TRNAAV77Thermus thermophilus HB8
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  • Entity ID: 23
    MoleculeChainsLengthOrganismImage
    MRNAAX11Thermus thermophilus HB8
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    Entity ID: 35
    MoleculeChainsLengthOrganismImage
    23S RIBOSOMAL RNABA2915Thermus thermophilus HB8
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    Entity ID: 36
    MoleculeChainsLengthOrganismImage
    5S RIBOSOMAL RNABB122Thermus thermophilus HB8
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FUA
    Query on FUA

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    AY
    FUSIDIC ACID
    C31 H48 O6
    IECPWNUMDGFDKC-MZJAQBGESA-N
     Ligand Interaction
    GDP
    Query on GDP

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    AY
    GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 7.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Revision History 

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2015-03-18
      Changes: Other
    • Version 2.0: 2017-08-02
      Changes: Atomic model, Data collection, Derived calculations
    • Version 2.1: 2019-12-11
      Changes: Other