4U67

Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel.

Wekselman, I.Zimmerman, E.Davidovich, C.Belousoff, M.Matzov, D.Krupkin, M.Rozenberg, H.Bashan, A.Friedlander, G.Kjeldgaard, J.Ingmer, H.Lindahl, L.Zengel, J.M.Yonath, A.

(2017) Structure 25: 1233-1241.e3

  • DOI: https://doi.org/10.1016/j.str.2017.06.004
  • Primary Citation of Related Structures:  
    4U67, 4WFN

  • PubMed Abstract: 

    Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin. The structure reveals a shift of the β hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within nascent chains trigger conformational rearrangements in the exit tunnel.


  • Organizational Affiliation

    Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2275Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3211Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4205Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5180Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6185Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13F [auth G]174Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXY1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14G [auth H]134Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15H [auth I]156Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSK9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16I [auth J]141Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17J [auth K]116Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18K [auth L]114Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19L [auth M]166Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20M [auth N]118Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21N [auth O]100Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22O [auth P]137Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23P [auth Q]95Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Q [auth R]114Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25R [auth S]237Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27S [auth T]91Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28T [auth U]81Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29U [auth V]67Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30V [auth W]55Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32W [auth Z]60Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33X [auth 1]55Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RSS4 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Y [auth 2]47Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35Z [auth 3]66Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 27
MoleculeChains LengthOrganismImage
23s RNAAA [auth X]2,880Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Entity ID: 28
MoleculeChains LengthOrganismImage
5s RNABA [auth Y]123Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth X]
AC [auth X]
BB [auth X]
CA [auth K]
CB [auth X]
AB [auth X],
AC [auth X],
BB [auth X],
CA [auth K],
CB [auth X],
DA [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 X],
JA [auth X],
JB [auth X],
KA [auth X],
KB [auth X],
LA [auth X],
LB [auth X],
MA [auth X],
MB [auth X],
NA [auth X],
NB [auth X],
OA [auth X],
OB [auth X],
PA [auth X],
PB [auth X],
QA [auth X],
QB [auth X],
RA [auth X],
RB [auth X],
SA [auth X],
SB [auth X],
TA [auth X],
TB [auth X],
UA [auth X],
UB [auth X],
VA [auth X],
VB [auth X],
WA [auth X],
WB [auth X],
XA [auth X],
XB [auth X],
YA [auth X],
YB [auth X],
ZA [auth X],
ZB [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.72α = 90
b = 412.591β = 90
c = 696.974γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description