5DM6

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.

Kaminishi, T.Schedlbauer, A.Fabbretti, A.Brandi, L.Ochoa-Lizarralde, B.He, C.G.Milon, P.Connell, S.R.Gualerzi, C.O.Fucini, P.

(2015) Nucleic Acids Res 43: 10015-10025

  • DOI: https://doi.org/10.1093/nar/gkv975
  • Primary Citation of Related Structures:  
    5DM6, 5DM7

  • PubMed Abstract: 

    Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.


  • Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1A [auth 0]224Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSS8 (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 L2B [auth A]274Deinococcus radioduransMutation(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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3C [auth B]205Deinococcus radioduransMutation(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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4D [auth C]197Deinococcus radioduransMutation(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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5E [auth D]177Deinococcus radioduransMutation(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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6F [auth E]171Deinococcus radioduransMutation(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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11G [auth F]144Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSS7 (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 L13H [auth G]142Deinococcus radioduransMutation(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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth H]134Deinococcus radioduransMutation(s): 0 
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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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth I]141Deinococcus radioduransMutation(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: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth J]136Deinococcus radioduransMutation(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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth K]113Deinococcus radioduransMutation(s): 0 
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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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth L]104Deinococcus radioduransMutation(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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth M]109Deinococcus radioduransMutation(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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth N]117Deinococcus radioduransMutation(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: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth O]94Deinococcus radioduransMutation(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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth P]127Deinococcus radioduransMutation(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: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth Q]93Deinococcus radioduransMutation(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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth R]110Deinococcus radioduransMutation(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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25T [auth S]175Deinococcus radioduransMutation(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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth T]84Deinococcus radioduransMutation(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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth U]72Deinococcus radioduransMutation(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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth V]66Deinococcus radioduransMutation(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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth W]55Deinococcus radioduransMutation(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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Y [auth Z]57Deinococcus radioduransMutation(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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33Z [auth 1]54Deinococcus radioduransMutation(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))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AA [auth 2]47Deinococcus radioduransMutation(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: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BA [auth 3]65Deinococcus radioduransMutation(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: 29
MoleculeChains LengthOrganismImage
23S ribosomal RNACA [auth X]2,881Deinococcus radiodurans
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Entity ID: 30
MoleculeChains LengthOrganismImage
5S ribosomal RNADA [auth Y]122Deinococcus radiodurans
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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]
AD [auth X]
AE [auth X]
AF [auth X]
AB [auth X],
AC [auth X],
AD [auth X],
AE [auth X],
AF [auth X],
AG [auth X],
AH [auth X],
BB [auth X],
BC [auth X],
BD [auth X],
BE [auth X],
BF [auth X],
BG [auth X],
BH [auth X],
CB [auth X],
CC [auth X],
CD [auth X],
CE [auth X],
CF [auth X],
CG [auth X],
CH [auth X],
DB [auth X],
DC [auth X],
DD [auth X],
DE [auth X],
DF [auth X],
DG [auth X],
DH [auth X],
EA [auth M],
EB [auth X],
EC [auth X],
ED [auth X],
EE [auth X],
EF [auth X],
EG [auth X],
EH [auth X],
FA [auth X],
FB [auth X],
FC [auth X],
FD [auth X],
FE [auth X],
FF [auth X],
FG [auth X],
FH [auth X],
GA [auth X],
GB [auth X],
GC [auth X],
GD [auth X],
GE [auth X],
GF [auth X],
GG [auth X],
GH [auth X],
HA [auth X],
HB [auth X],
HC [auth X],
HD [auth X],
HE [auth X],
HF [auth X],
HG [auth X],
HH [auth X],
IA [auth X],
IB [auth X],
IC [auth X],
ID [auth X],
IE [auth X],
IF [auth X],
IG [auth X],
IH [auth X],
JA [auth X],
JB [auth X],
JC [auth X],
JD [auth X],
JE [auth X],
JF [auth X],
JG [auth X],
JH [auth X],
KA [auth X],
KB [auth X],
KC [auth X],
KD [auth X],
KE [auth X],
KF [auth X],
KG [auth X],
KH [auth X],
LA [auth X],
LB [auth X],
LC [auth X],
LD [auth X],
LE [auth X],
LF [auth X],
LG [auth X],
LH [auth X],
MA [auth X],
MB [auth X],
MC [auth X],
MD [auth X],
ME [auth X],
MF [auth X],
MG [auth X],
MH [auth X],
NA [auth X],
NB [auth X],
NC [auth X],
ND [auth X],
NE [auth X],
NF [auth X],
NG [auth X],
NH [auth X],
OA [auth X],
OB [auth X],
OC [auth X],
OD [auth X],
OE [auth X],
OF [auth X],
OG [auth X],
OH [auth X],
PA [auth X],
PB [auth X],
PC [auth X],
PD [auth X],
PE [auth X],
PF [auth X],
PG [auth X],
PH [auth Y],
QA [auth X],
QB [auth X],
QC [auth X],
QD [auth X],
QE [auth X],
QF [auth X],
QG [auth X],
QH [auth Y],
RA [auth X],
RB [auth X],
RC [auth X],
RD [auth X],
RE [auth X],
RF [auth X],
RG [auth X],
RH [auth Y],
SA [auth X],
SB [auth X],
SC [auth X],
SD [auth X],
SE [auth X],
SF [auth X],
SG [auth X],
SH [auth Y],
TA [auth X],
TB [auth X],
TC [auth X],
TD [auth X],
TE [auth X],
TF [auth X],
TG [auth X],
TH [auth Y],
UA [auth X],
UB [auth X],
UC [auth X],
UD [auth X],
UE [auth X],
UF [auth X],
UG [auth X],
VA [auth X],
VB [auth X],
VC [auth X],
VD [auth X],
VE [auth X],
VF [auth X],
VG [auth X],
WA [auth X],
WB [auth X],
WC [auth X],
WD [auth X],
WE [auth X],
WF [auth X],
WG [auth X],
XA [auth X],
XB [auth X],
XC [auth X],
XD [auth X],
XE [auth X],
XF [auth X],
XG [auth X],
YA [auth X],
YB [auth X],
YC [auth X],
YD [auth X],
YE [auth X],
YF [auth X],
YG [auth X],
ZA [auth X],
ZB [auth X],
ZC [auth X],
ZD [auth X],
ZE [auth X],
ZF [auth X],
ZG [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.9α = 90
b = 410.76β = 90
c = 696.12γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2016-02-03
    Changes: Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary