4V4J

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.327 
  • R-Value Observed: 0.327 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.

Korostelev, A.Trakhanov, S.Asahara, H.Laurberg, M.Lancaster, L.Noller, H.F.

(2007) Proc Natl Acad Sci U S A 104: 16840-16843

  • DOI: 10.1073/pnas.0707850104
  • Primary Citation of Related Structures:  
    4V4J

  • PubMed Abstract: 
  • The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that during the first step of translocation, the SD helix moves along its helical screw axis ...

    The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that during the first step of translocation, the SD helix moves along its helical screw axis. Contacts between the SD helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of 16S rRNA. Contact with the neck (helix 28) of the 30S subunit near its hinge point suggests that formation of the SD helix could affect positioning of the head of the 30S subunit for optimal interaction with initiator tRNA. The bulged U723 in helix 23a interacts with the minor groove of the SD helix at the C1539.G-10 base pair, explaining its selective conservation in bacteria and archaea.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95060, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1 A229Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplATT_C1739
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 B276Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 C206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 D205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 E182Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 F180Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
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Entity ID: 9
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50S ribosomal protein L9 G148Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplITT_C1743
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 H140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 I122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 J150Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 K141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 L118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 M112Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 N146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplSTT_C0669
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 O118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplTTT_C0185
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 P101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 Q113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplVTT_C1323
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Entity ID: 20
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50S ribosomal protein L23 R96Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplWTT_C1326
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 S110Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 T206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27 U85Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
LSU ribosomal protein L28P V98Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 W72Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
LSU ribosomal protein L30P X60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 Y60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 Z49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 a65Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmITT_C0184
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 b37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 c256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 d239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 e209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 f162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 g101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
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Entity ID: 40
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30S ribosomal protein S7 h156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 i138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
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Entity ID: 42
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30S ribosomal protein S9 j128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 k105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 l129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 m132Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
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Entity ID: 46
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30S ribosomal protein S13 n126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
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Entity ID: 47
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30S ribosomal protein S14 type Z o61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
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Entity ID: 48
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30S ribosomal protein S15 p89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
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Entity ID: 49
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30S ribosomal protein S16 q88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
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Entity ID: 50
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30S ribosomal protein S17 r105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
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Entity ID: 51
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30S ribosomal protein S18 s88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
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Entity ID: 52
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30S ribosomal protein S19 t93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
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Entity ID: 53
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30S ribosomal protein S20 u106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
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Entity ID: 54
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30S ribosomal protein Thx v27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsUTT_C1030
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S LARGE SUBUNIT RIBOSOMAL RNAw2889Thermus thermophilus HB27
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Entity ID: 2
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5S LARGE SUBUNIT RIBOSOMAL RNAx120Thermus thermophilus HB27
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Entity ID: 31
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16S RNAy1522Thermus thermophilus HB27
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Entity ID: 32
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P-site tRNAfMETz77Thermus thermophilus HB27
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Entity ID: 33
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E-site tRNA276Thermus thermophilus HB27
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  • Entity ID: 34
    MoleculeChainsLengthOrganismImage
    MRNA318Thermus thermophilus HB27
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.83 Å
    • R-Value Free: 0.351 
    • R-Value Work: 0.327 
    • R-Value Observed: 0.327 
    • Space Group: I 4 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 507.21α = 90
    b = 507.21β = 90
    c = 692.51γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    PDB_EXTRACTdata extraction
    ADSCdata collection
    CNSrefinement
    d*TREKdata reduction
    SCALAdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other