2ZJP

Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.300 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • 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: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33A [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: 2
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50S RIBOSOMAL PROTEIN L34B [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: 3
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50S RIBOSOMAL PROTEIN L35C [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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36D [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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NOSIHEPTIDEE [auth 5]13Streptomyces actuosusMutation(s): 0 
Gene Names: nosM
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Entity ID: 6
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50S RIBOSOMAL PROTEIN L2F [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: 7
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50S RIBOSOMAL PROTEIN L3G [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: 8
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50S RIBOSOMAL PROTEIN L4H [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: 9
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50S RIBOSOMAL PROTEIN L5I [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: 10
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50S RIBOSOMAL PROTEIN L6J [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: 11
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50S RIBOSOMAL PROTEIN L11K [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: 12
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50S RIBOSOMAL PROTEIN L13L [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: 13
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50S RIBOSOMAL PROTEIN L14M [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: 14
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50S RIBOSOMAL PROTEIN L15N [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: 15
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50S RIBOSOMAL PROTEIN L16O [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: 16
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50S RIBOSOMAL PROTEIN L17P [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: 17
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50S RIBOSOMAL PROTEIN L18Q [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: 18
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50S RIBOSOMAL PROTEIN L19R [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: 19
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50S RIBOSOMAL PROTEIN L20S [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: 20
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50S RIBOSOMAL PROTEIN L21T [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: 21
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50S RIBOSOMAL PROTEIN L22U [auth P]134Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ7 (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 L23V [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: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24W [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: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25X [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: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27Y [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: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28Z [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: 27
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50S RIBOSOMAL PROTEIN L29AA [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: 28
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50S RIBOSOMAL PROTEIN L30BA [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: 30
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50S RIBOSOMAL PROTEIN L32DA [auth Y]60Deinococcus 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: 29
MoleculeChainsLengthOrganismImage
RIBOSOMAL 23S RNACA [auth X]2880Deinococcus radiodurans
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Entity ID: 31
MoleculeChainsLengthOrganismImage
RIBOSOMAL 5S RNAEA [auth Z]123Deinococcus radiodurans
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO1
Query on NO1

Download Ideal Coordinates CCD File 
GA [auth 5]4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid
C11 H11 N O3
BSECKLZXEJBFRE-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth 4], KB [auth Y]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth X] , BB [auth X] , CB [auth X] , DB [auth X] , EB [auth X] , FB [auth X] , GB [auth X] , HA [auth M] , 
AB [auth X],  BB [auth X],  CB [auth X],  DB [auth X],  EB [auth X],  FB [auth X],  GB [auth X],  HA [auth M],  HB [auth X],  IA [auth X],  IB [auth X],  JA [auth X],  JB [auth X],  KA [auth X],  LA [auth X],  LB [auth Z],  MA [auth X],  MB [auth Z],  NA [auth X],  NB [auth Z],  OA [auth X],  OB [auth Z],  PA [auth X],  PB [auth Z],  QA [auth X],  QB [auth Z],  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
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
3GL
Query on 3GL
E [auth 5]L-PEPTIDE LINKINGC5 H9 N O5GLU
BB9
Query on BB9
E [auth 5]PEPTIDE LINKINGC3 H5 N O2 SCYS
DBU
Query on DBU
E [auth 5]PEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
E [auth 5]PEPTIDE LINKINGC3 H5 N O2SER
MH6
Query on MH6
E [auth 5]PEPTIDE LINKINGC3 H5 N O3SER
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000221
Query on PRD_000221
E [auth 5]NosiheptideThiopeptide /  Antibiotic

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.300 
  • 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
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: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2011-11-30
    Changes: Database references
  • Version 1.5: 2011-12-28
    Changes: Atomic model, Derived calculations
  • Version 1.6: 2012-12-12
    Changes: Other
  • Version 2.0: 2019-10-16
    Changes: Data collection, Derived calculations, Polymer sequence, Structure summary