2ZJR

Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.

Harms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.

(2008) Mol Cell 30: 26-38

  • DOI: 10.1016/j.molcel.2008.01.009
  • Primary Citation of Related Structures:  
    2ZJR, 2ZJP, 2ZJQ, 3CF5

  • PubMed Abstract: 
  • The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit ...

    The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G' subdomain of EF-G to regulate EF-G turnover during protein synthesis.


    Organizational Affiliation

    Cluster of Excellence for Macromolecular Complexes, Institut für Organische Chemie und Chemische Biologie, J.W. Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]274Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ9 (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: 4
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50S ribosomal protein L3D [auth B]211Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXK2 (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: 5
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50S ribosomal protein L4E [auth C]205Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXK1 (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: 6
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50S ribosomal protein L5F [auth D]180Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ0 (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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]185Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSL3 (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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11H [auth F]144Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSS7 (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
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50S ribosomal protein L13I [auth G]174Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXY1 (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: 10
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50S ribosomal protein L14J [auth H]134Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ2 (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: 11
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50S ribosomal protein L15K [auth I]156Deinococcus radioduransMutation(s): 0 
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: 12
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50S ribosomal protein L16L [auth J]142Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ5 (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
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50S ribosomal protein L17M [auth K]116Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSJ5 (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: 14
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50S ribosomal protein L18N [auth L]114Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSL2 (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: 15
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50S ribosomal protein L19O [auth M]166Deinococcus radioduransMutation(s): 0 
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: 16
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50S ribosomal protein L20P [auth N]118Deinococcus radioduransMutation(s): 0 
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: 17
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50S ribosomal protein L21Q [auth O]100Deinococcus radioduransMutation(s): 0 
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: 18
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50S ribosomal protein L22R [auth P]134Deinococcus radioduransMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L23S [auth Q]95Deinococcus radioduransMutation(s): 0 
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: 20
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50S ribosomal protein L24T [auth R]115Deinococcus radioduransMutation(s): 0 
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: 21
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50S ribosomal protein L25U [auth S]237Deinococcus radioduransMutation(s): 0 
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: 22
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50S ribosomal protein L27V [auth T]91Deinococcus radioduransMutation(s): 0 
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: 23
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50S ribosomal protein L28W [auth U]81Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RRG8 (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
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50S ribosomal protein L29X [auth V]67Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ4 (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: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth W]55Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSL0 (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: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32Z60Deinococcus radioduransMutation(s): 0 
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: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth 1]55Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSS4 (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 L34BA [auth 2]47Deinococcus radioduransMutation(s): 0 
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: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth 3]66Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSW6 (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 L36DA [auth 4]37Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSK0 (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: 1
MoleculeChainsLengthOrganismImage
ribosomal 23S RNAA [auth X]2880Deinococcus radiodurans
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Entity ID: 2
MoleculeChainsLengthOrganismImage
ribosomal 5S RNAB [auth Y]123Deinococcus radiodurans
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth X] , BB [auth X] , CB [auth X] , DB [auth X] , EA [auth X] , EB [auth X] , FA [auth X] , FB [auth X] , 
AB [auth X],  BB [auth X],  CB [auth X],  DB [auth X],  EA [auth X],  EB [auth X],  FA [auth X],  FB [auth X],  GA [auth X],  GB [auth X],  HA [auth X],  HB [auth X],  IA [auth X],  IB [auth Y],  JA [auth X],  JB [auth Y],  KA [auth X],  KB [auth Y],  LA [auth X],  LB [auth Y],  MA [auth X],  MB [auth Y],  NA [auth X],  OA [auth X],  PA [auth X],  QA [auth X],  RA [auth X],  SA [auth X],  TA [auth X],  UA [auth X],  VA [auth X],  WA [auth X],  XA [auth X],  YA [auth X],  ZA [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.277 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.9α = 90
b = 408.9β = 90
c = 694.5γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance