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 L1C [auth A]229Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplATT_C1739
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Entity ID: 4
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50S ribosomal protein L2D [auth B]276Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth C]206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth D]205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth E]182Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth F]180Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth G]148Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplITT_C1743
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth H]140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth I]122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth J]150Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
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Entity ID: 13
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50S ribosomal protein L16M [auth K]141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth L]118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth M]112Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth N]146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplSTT_C0669
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth O]118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplTTT_C0185
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth P]101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth Q]113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplVTT_C1323
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth R]96Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplWTT_C1326
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth S]110Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth T]206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth U]85Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
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Entity ID: 24
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LSU ribosomal protein L28PX [auth V]98Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth W]72Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
LSU ribosomal protein L30PZ [auth X]60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth Y]60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth Z]49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth a]65Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmITT_C0184
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth b]37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth c]256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth d]239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth e]209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth f]162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth g]101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth h]156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth i]138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth j]128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth k]105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
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Entity ID: 44
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30S ribosomal protein S11RA [auth l]129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
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Entity ID: 45
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30S ribosomal protein S12SA [auth m]132Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
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Entity ID: 46
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30S ribosomal protein S13TA [auth n]126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
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Entity ID: 47
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30S ribosomal protein S14 type ZUA [auth o]61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
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Entity ID: 48
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30S ribosomal protein S15VA [auth p]89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
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Entity ID: 49
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30S ribosomal protein S16WA [auth q]88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth r]105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
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Entity ID: 51
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30S ribosomal protein S18YA [auth s]88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
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Entity ID: 52
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30S ribosomal protein S19ZA [auth t]93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
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Entity ID: 53
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30S ribosomal protein S20AB [auth u]106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
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Entity ID: 54
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30S ribosomal protein ThxBB [auth v]27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsUTT_C1030
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Entity ID: 1
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23S LARGE SUBUNIT RIBOSOMAL RNAA [auth w]2889Thermus thermophilus HB27
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Entity ID: 2
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5S LARGE SUBUNIT RIBOSOMAL RNAB [auth x]120Thermus thermophilus HB27
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Entity ID: 31
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16S RNAEA [auth y]1522Thermus thermophilus HB27
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Entity ID: 32
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P-site tRNAfMETFA [auth z]77Thermus thermophilus HB27
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Entity ID: 33
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E-site tRNAGA [auth 2]76Thermus thermophilus HB27
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  • Entity ID: 34
    MoleculeChainsLengthOrganismImage
    MRNAHA [auth 3]18Thermus thermophilus HB27
    Protein Feature View
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    • Reference Sequence
    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