4V42

Crystal structure of the ribosome at 5.5 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the ribosome at 5.5 A resolution

Yusupov, M.M.Yusupova, G.Z.Baucom, A.Lieberman, K.Earnest, T.N.Cate, J.H.D.Noller, H.F.

(2001) Science 292: 883-896

  • DOI: 10.1126/science.1060089
  • Primary Citation of Related Structures:  
    4V42

  • PubMed Abstract: 
  • We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map ...

    We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.


    Organizational Affiliation

    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2F [auth AE]256Thermus thermophilusMutation(s): 0 
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Entity ID: 6
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30S RIBOSOMAL PROTEIN S3G [auth AF]239Thermus thermophilusMutation(s): 0 
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Entity ID: 7
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30S RIBOSOMAL PROTEIN S4H [auth AG]209Thermus thermophilusMutation(s): 0 
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S5I [auth AH]162Thermus thermophilusMutation(s): 0 
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S6J [auth AI]101Thermus thermophilusMutation(s): 0 
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S7K [auth AJ]156Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S8L [auth AK]138Thermus thermophilusMutation(s): 0 
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S9M [auth AL]128Thermus thermophilusMutation(s): 0 
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S10N [auth AM]105Thermus thermophilusMutation(s): 0 
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S11O [auth AN]129Thermus thermophilusMutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S12P [auth AO]135Thermus thermophilusMutation(s): 0 
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S13Q [auth AP]126Thermus thermophilusMutation(s): 0 
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Entity ID: 17
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30S RIBOSOMAL PROTEIN S14R [auth AQ]61Thermus thermophilusMutation(s): 0 
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S15S [auth AR]89Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16T [auth AS]91Thermus thermophilusMutation(s): 0 
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S17U [auth AT]105Thermus thermophilusMutation(s): 0 
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Entity ID: 21
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30S RIBOSOMAL PROTEIN S18V [auth AU]88Thermus thermophilusMutation(s): 0 
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Entity ID: 22
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30S RIBOSOMAL PROTEIN S19W [auth AV]93Thermus thermophilusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20X [auth AW]106Thermus thermophilusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXY [auth AX]26Thermus thermophilusMutation(s): 0 
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L1BA [auth BC]228Thermus thermophilusMutation(s): 0 
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Entity ID: 28
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50S RIBOSOMAL PROTEIN L2CA [auth BD]178Thermus thermophilusMutation(s): 0 
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Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
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50S RIBOSOMAL PROTEIN L3DA [auth BE]338Thermus thermophilusMutation(s): 0 
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L4EA [auth BF]246Thermus thermophilusMutation(s): 0 
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L5FA [auth BG]176Thermus thermophilusMutation(s): 0 
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L6GA [auth BH]177Thermus thermophilusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7/L12HA [auth BI], IA [auth BJ]128Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P29396 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9JA [auth BK]149Thermus thermophilusMutation(s): 0 
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Entity ID: 35
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50S RIBOSOMAL PROTEIN L11KA [auth BL]141Thermus thermophilusMutation(s): 0 
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Entity ID: 36
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50S RIBOSOMAL PROTEIN L13LA [auth BM]145Thermus thermophilusMutation(s): 0 
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Entity ID: 37
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50S RIBOSOMAL PROTEIN L14MA [auth BN]122Thermus thermophilusMutation(s): 0 
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Entity ID: 38
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50S RIBOSOMAL PROTEIN L15NA [auth BO]164Thermus thermophilusMutation(s): 0 
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Entity ID: 39
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50S RIBOSOMAL PROTEIN L16OA [auth BP]138Thermus thermophilusMutation(s): 0 
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Entity ID: 40
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50S RIBOSOMAL PROTEIN L18PA [auth BQ]186Thermus thermophilusMutation(s): 0 
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L19QA [auth BR]66Thermus thermophilusMutation(s): 0 
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Entity ID: 42
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50S RIBOSOMAL PROTEIN L22RA [auth BS]113Thermus thermophilusMutation(s): 0 
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L23SA [auth BT]84Thermus thermophilusMutation(s): 0 
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Entity ID: 44
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50S RIBOSOMAL PROTEIN L24TA [auth BU]119Thermus thermophilusMutation(s): 0 
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Entity ID: 45
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50S RIBOSOMAL PROTEIN L25UA [auth BV]94Thermus thermophilusMutation(s): 0 
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L29VA [auth BW]70Thermus thermophilusMutation(s): 0 
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Entity ID: 47
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50S RIBOSOMAL PROTEIN L30WA [auth BX]60Thermus thermophilusMutation(s): 0 
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Entity ID: 1
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30S 16S RIBOSOMAL RNAA [auth AA]1522Thermus thermophilus
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Entity ID: 2
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TRNA(PHE)B [auth AB], C [auth AC]76N/A
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Entity ID: 3
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TRNA(PHE)D [auth AD]74N/A
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    A- AND P-SITE MESSENGER RNA CODONSE [auth A1]6N/A
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    Entity ID: 25
    MoleculeChainsLengthOrganismImage
    50S 23S RIBOSOMAL RNAZ [auth BA]2916Thermus thermophilus
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    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    50S 5S RIBOSOMAL RNAAA [auth BB]123Thermus thermophilus
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    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 5.50 Å
    • Space Group: I 4 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 507.2α = 90
    b = 507.2β = 90
    c = 803.66γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    CCP4model building
    Omodel building
    CCP4phasing

    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