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 

Starting Models: experimental
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This is version 1.3 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth A]229Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth B]276Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth C]206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth D]205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth E]182Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth F]180Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth G]148Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth H]140Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth I]122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth J]150Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth K]141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth L]118Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth M]112Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth N]146Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth O]118Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth P]101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth Q]113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth R]96Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth S]110Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth T]206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth U]85Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L28PX [auth V]98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth W]72Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L30PZ [auth X]60Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth Y]60Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth Z]49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth a]65Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth b]37Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth c]256Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth d]239Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth e]209Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth f]162Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth g]101Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth h]156Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth i]138Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth j]128Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth k]105Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth l]129Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth m]132Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth n]126Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZUA [auth o]61Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth p]89Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth q]88Thermus thermophilus HB27Mutation(s): 0 
UniProt
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UniProt GroupQ5SJH3
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth r]105Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP0DOY7
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth s]88Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SLQ0
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth t]93Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHP2
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth u]106Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP80380
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxBB [auth v]27Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SIH3
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S LARGE SUBUNIT RIBOSOMAL RNAA [auth w]2,889Thermus thermophilus HB27
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S LARGE SUBUNIT RIBOSOMAL RNAB [auth x]120Thermus thermophilus HB27
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Entity ID: 31
MoleculeChains LengthOrganismImage
16S RNAEA [auth y]1,522Thermus thermophilus HB27
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Entity ID: 32
MoleculeChains LengthOrganismImage
P-site tRNAfMETFA [auth z]77Thermus thermophilus HB27
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Entity ID: 33
MoleculeChains LengthOrganismImage
E-site tRNAGA [auth 2]76Thermus thermophilus HB27
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Entity ID: 34
MoleculeChains LengthOrganismImage
MRNAHA [auth 3]18Thermus thermophilus HB27
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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



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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
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Data collection, Structure summary