2OTJ

13-deoxytedanolide bound to the large subunit of Haloarcula marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 

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This is version 1.4 of the entry. See complete history


Literature

The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole.

Schroeder, S.J.Blaha, G.Tirado-Rives, J.Steitz, T.A.Moore, P.B.

(2007) J Mol Biol 367: 1471-1479

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.081
  • Primary Citation of Related Structures:  
    2OTJ, 2OTL

  • PubMed Abstract: 

    Crystal structures of the 50 S ribosomal subunit from Haloarcula marismortui complexed with two antibiotics have identified new sites at which antibiotics interact with the ribosome and inhibit protein synthesis. 13-Deoxytedanolide binds to the E site of the 50 S subunit at the same location as the CCA of tRNA, and thus appears to inhibit protein synthesis by competing with deacylated tRNAs for E site binding. Girodazole binds near the E site region, but is somewhat buried and may inhibit tRNA binding by interfering with conformational changes that occur at the E site. The specificity of 13-deoxytedanolide for eukaryotic ribosomes is explained by its extensive interactions with protein L44e, which is an E site component of archaeal and eukaryotic ribosomes, but not of eubacterial ribosomes. In addition, protein L28, which is unique to the eubacterial E site, overlaps the site occupied by 13-deoxytedanolide, precluding its binding to eubacterial ribosomes. Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria.


  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2PC [auth A]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3PD [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4PE [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]178Haloarcula marismortuiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeH [auth F]120Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EI [auth G]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth H]171Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PK [auth J]145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PL [auth K]132Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PM [auth L]165Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eN [auth M]194Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PO [auth N]187Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eP [auth O]116Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19eQ [auth P]149Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eR [auth Q]96Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PS [auth R]155Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PT [auth S]85Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PU [auth T]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24eV [auth U]66Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PW [auth V]71Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PX [auth W]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eY [auth X]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32eZ [auth Y]241Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37AeAA [auth Z]73Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eBA [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eCA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44EDA [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11PEA [auth I]161Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
13T
Query on 13T

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FA [auth 0]13-DEOXYTEDANOLIDE
C32 H50 O10
YTOSLGBJMGPGPA-AYJAMTIUSA-N
CD
Query on CD

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CJ [auth 3],
MI [auth O],
UI [auth U],
YI [auth Z],
ZI [auth 1]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

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KE [auth 0],
LE [auth 0]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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DI [auth J]
DJ [auth 3]
EI [auth J]
FI [auth J]
IH [auth 0]
DI [auth J],
DJ [auth 3],
EI [auth J],
FI [auth J],
IH [auth 0],
II [auth L],
JH [auth 0],
KH [auth 0],
KI [auth M],
LH [auth 0],
LI [auth N],
MH [auth 0],
NH [auth 0],
NI [auth O],
OH [auth 0],
PH [auth 0],
QH [auth 0],
RI [auth R],
WI [auth Y],
XH [auth A],
XI [auth Y],
ZH [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AB [auth 0]
AC [auth 0]
AD [auth 0]
AE [auth 0]
AJ [auth 3]
AB [auth 0],
AC [auth 0],
AD [auth 0],
AE [auth 0],
AJ [auth 3],
BB [auth 0],
BC [auth 0],
BD [auth 0],
BE [auth 0],
BJ [auth 3],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
FB [auth 0],
FC [auth 0],
FD [auth 0],
FE [auth 0],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
GE [auth 0],
GI [auth K],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HD [auth 0],
HE [auth 0],
IA [auth 0],
IB [auth 0],
IC [auth 0],
ID [auth 0],
IE [auth 0],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JD [auth 0],
JE [auth 0],
KA [auth 0],
KB [auth 0],
KC [auth 0],
KD [auth 0],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LD [auth 0],
MA [auth 0],
MB [auth 0],
MC [auth 0],
MD [auth 0],
NA [auth 0],
NB [auth 0],
NC [auth 0],
ND [auth 0],
OA [auth 0],
OB [auth 0],
OC [auth 0],
OD [auth 0],
PA [auth 0],
PB [auth 0],
PC [auth 0],
PD [auth 0],
QA [auth 0],
QB [auth 0],
QC [auth 0],
QD [auth 0],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RD [auth 0],
RH [auth 9],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TD [auth 0],
TI [auth T],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UD [auth 0],
UH [auth A],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
VH [auth A],
VI [auth Y],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
YH [auth B],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AF [auth 0]
AG [auth 0]
AH [auth 0]
AI [auth C]
BF [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
AI [auth C],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth H],
CF [auth 0],
CG [auth 0],
CH [auth 0],
CI [auth J],
DF [auth 0],
DG [auth 0],
DH [auth 0],
EF [auth 0],
EG [auth 0],
EH [auth 0],
FF [auth 0],
FG [auth 0],
FH [auth 0],
GF [auth 0],
GG [auth 0],
GH [auth 0],
HF [auth 0],
HG [auth 0],
HH [auth 0],
HI [auth L],
IF [auth 0],
IG [auth 0],
JF [auth 0],
JG [auth 0],
JI [auth M],
KF [auth 0],
KG [auth 0],
LF [auth 0],
LG [auth 0],
ME [auth 0],
MF [auth 0],
MG [auth 0],
NE [auth 0],
NF [auth 0],
NG [auth 0],
OE [auth 0],
OF [auth 0],
OG [auth 0],
OI [auth Q],
PE [auth 0],
PF [auth 0],
PG [auth 0],
PI [auth R],
QE [auth 0],
QF [auth 0],
QG [auth 0],
QI [auth R],
RE [auth 0],
RF [auth 0],
RG [auth 0],
SE [auth 0],
SF [auth 0],
SG [auth 0],
SH [auth 9],
SI [auth S],
TE [auth 0],
TF [auth 0],
TG [auth 0],
TH [auth 9],
UE [auth 0],
UF [auth 0],
UG [auth 0],
VE [auth 0],
VF [auth 0],
VG [auth 0],
WE [auth 0],
WF [auth 0],
WG [auth 0],
WH [auth A],
XE [auth 0],
XF [auth 0],
XG [auth 0],
YE [auth 0],
YF [auth 0],
YG [auth 0],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.738α = 90
b = 299.519β = 90
c = 573.593γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description