1NKW

Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High resolution structure of the large ribosomal subunit from a mesophilic eubacterium

Harms, J.M.Schluenzen, F.Zarivach, R.Bashan, A.Gat, S.Agmon, I.Bartels, H.Franceschi, F.Yonath, A.

(2001) Cell 107: 679-688

  • DOI: 10.1016/s0092-8674(01)00546-3
  • Primary Citation of Related Structures:  
    1NKW

  • PubMed Abstract: 
  • We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins ...

    We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.


    Related Citations: 
    • Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria
      Schluenzen, F., Zarivach, R., Harms, J.M., Bashan, A., Tocilj, A., Albrecht, R., Yonath, A., Franceschi, F.
      (2001) Nature 413: 814

    Organizational Affiliation

    Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603, Hamburg, Germany.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]275Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 4
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50S ribosomal protein L3D [auth B]211Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]205Deinococcus radioduransMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]180Deinococcus radioduransMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]212Deinococcus radioduransMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L9H [auth F]146Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RY49 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11I [auth G]144Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 10
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50S ribosomal protein L13J [auth H]174Deinococcus radioduransMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth I]134Deinococcus radioduransMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth J]156Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSK9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth K]142Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 14
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50S ribosomal protein L17N [auth L]116Deinococcus radioduransMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth M]114Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth N]166Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 17
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50S ribosomal protein L20Q [auth O]118Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth P]100Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth Q]134Deinococcus radioduransMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth R]95Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth S]115Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
general stress protein CTCV [auth T]253Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth U]91Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth W]67Deinococcus radioduransMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L30Y [auth X]55Deinococcus radioduransMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L31Z [auth Y]73Deinococcus radioduransMutation(s): 0 
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Find proteins for Q9RW44 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 27
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50S ribosomal protein L32AA [auth Z]60Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth 1]82Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 2]47Deinococcus radioduransMutation(s): 0 
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Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 3]64Deinococcus radioduransMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth 4]36Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 0]2,880Deinococcus radiodurans
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 9]124Deinococcus radiodurans
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170α = 90
b = 410β = 90
c = 697γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance