5JVH

The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.

Krupkin, M.Wekselman, I.Matzov, D.Eyal, Z.Diskin Posner, Y.Rozenberg, H.Zimmerman, E.Bashan, A.Yonath, A.

(2016) Proc Natl Acad Sci U S A 113: E6796-E6805

  • DOI: 10.1073/pnas.1614297113
  • Primary Citation of Related Structures:  
    5JVG, 5JVH

  • PubMed Abstract: 
  • Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them ...

    Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA-namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16-these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel ada.yonath@weizmann.ac.il.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]275Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplBDR_0314
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]211Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplCDR_0311
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]205Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplDDR_0312
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]180Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplEDR_0323
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]185Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplFDR_2111
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth G]174Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplMDR_0174
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth H]134Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplNDR_0321
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth I]156Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplODR_2115
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: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth J]141Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplPDR_0318
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth K]116Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplQDR_2129
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth L]114Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplRDR_2112
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth M]166Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplSDR_0755
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: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth N]118Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplTDR_2004
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: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth O]100Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplUDR_0086
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: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth P]134Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplVDR_0316
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth Q]95Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplWDR_0313
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth R]115Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplXDR_0322
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25T [auth S]237Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplYctcDR_0427
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: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth T]91Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmADR_0085
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: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth U]81Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmBDR_2524
UniProt
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: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth V]67Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmCDR_0319
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth W]55Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmDDR_2114
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32Y [auth Z]60Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmFDR_2366
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: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33Z [auth 1]54Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmGDR_2049
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34AA [auth 2]47Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmHDR_2152
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35BA [auth 3]66Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmIDR_2005
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth X]2,880Deinococcus radiodurans R1
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth Y]123Deinococcus radiodurans R1
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6O1
Query on 6O1

Download Ideal Coordinates CCD File 
CA [auth X]Evernimicin
C70 H97 Cl2 N O38
UPADRKHAIMTUCC-PPTKMMIPSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth X],
AC [auth X],
AD [auth X],
AE [auth X],
BB [auth X],
AB [auth X],
AC [auth X],
AD [auth X],
AE [auth X],
BB [auth X],
BC [auth X],
BD [auth X],
BE [auth X],
CB [auth X],
CC [auth X],
CD [auth X],
CE [auth X],
DA [auth X],
DB [auth X],
DC [auth X],
DD [auth X],
DE [auth X],
EA [auth X],
EB [auth X],
EC [auth X],
ED [auth X],
EE [auth X],
FA [auth X],
FB [auth X],
FC [auth X],
FD [auth X],
FE [auth X],
GA [auth X],
GB [auth X],
GC [auth X],
GD [auth X],
GE [auth X],
HA [auth X],
HB [auth X],
HC [auth X],
HD [auth X],
HE [auth X],
IA [auth X],
IB [auth X],
IC [auth X],
ID [auth X],
IE [auth X],
JA [auth X],
JB [auth X],
JC [auth X],
JD [auth X],
JE [auth X],
KA [auth X],
KB [auth X],
KC [auth X],
KD [auth X],
KE [auth X],
LA [auth X],
LB [auth X],
LC [auth X],
LD [auth X],
LE [auth X],
MA [auth X],
MB [auth X],
MC [auth X],
MD [auth X],
ME [auth X],
NA [auth X],
NB [auth X],
NC [auth X],
ND [auth X],
NE [auth X],
OA [auth X],
OB [auth X],
OC [auth X],
OD [auth X],
OE [auth X],
PA [auth X],
PB [auth X],
PC [auth X],
PD [auth X],
PE [auth X],
QA [auth X],
QB [auth X],
QC [auth X],
QD [auth X],
QE [auth X],
RA [auth X],
RB [auth X],
RC [auth X],
RD [auth X],
RE [auth X],
SA [auth X],
SB [auth X],
SC [auth X],
SD [auth X],
SE [auth Y],
TA [auth X],
TB [auth X],
TC [auth X],
TD [auth X],
TE [auth K],
UA [auth X],
UB [auth X],
UC [auth X],
UD [auth X],
UE [auth K],
VA [auth X],
VB [auth X],
VC [auth X],
VD [auth X],
VE [auth M],
WA [auth X],
WB [auth X],
WC [auth X],
WD [auth X],
XA [auth X],
XB [auth X],
XC [auth X],
XD [auth X],
YA [auth X],
YB [auth X],
YC [auth X],
YD [auth X],
ZA [auth X],
ZB [auth X],
ZC [auth X],
ZD [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.475α = 90
b = 407.38β = 90
c = 692.552γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-11-09 
  • Deposition Author(s): Yonath, A.

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release