3G71

Co-crystal structure of Bruceantin bound to the large ribosomal subunit

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.

Gurel, G., Blaha, G., Moore, P.B., Steitz, T.A.

(2009) J Mol Biol 389: 146-156

  • DOI: https://doi.org/10.1016/j.jmb.2009.04.005
  • Primary Citation of Related Structures:  
    3G4S, 3G6E, 3G71

  • PubMed Abstract: 

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2PB [auth A]237Haloarcula 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3PC [auth B]337Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4PD [auth C]246Haloarcula marismortuiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PE [auth D]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PF [auth E]172Haloarcula marismortuiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeG [auth F]119Haloarcula marismortuiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EH [auth G]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10eI [auth H]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11PJ [auth I]70Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PK [auth J]142Haloarcula marismortuiMutation(s): 0 
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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 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PM [auth L]165Haloarcula marismortuiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eN [auth M]194Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PO [auth N]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eP [auth O]115Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19eQ [auth P]143Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eR [auth Q]95Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PS [auth R]150Haloarcula 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]81Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PU [auth T]119Haloarcula 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]53Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PW [auth V]65Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PX [auth W]154Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eY [auth X]82Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32eZ [auth Y]142Haloarcula marismortuiMutation(s): 0 
UniProt
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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]56Haloarcula marismortuiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eCA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44EDA [auth 3]92Haloarcula marismortuiMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 0]2,923Haloarcula marismortui
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Entity ID: 31
MoleculeChains LengthOrganismImage
5S ribosomal RNAEA [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WIN
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CK [auth 0]methyl (5beta,7alpha,9beta,10alpha,11alpha,12alpha,13beta,15alpha)-15-{[(2E)-3,4-dimethylpent-2-enoyl]oxy}-3,11,12-trihydroxy-2,16-dioxo-13,20-epoxypicras-3-en-21-oate
C28 H36 O11
IRQXZTBHNKVIRL-GOTQHHPNSA-N
CD
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HL [auth U],
KL [auth Z],
LL [auth 1],
OL [auth 3],
YK [auth O]		CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SR
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AH [auth 0]
AI [auth 0]
AJ [auth 0]
AK [auth 0]
BH [auth 0]
AH [auth 0],
AI [auth 0],
AJ [auth 0],
AK [auth 0],
BH [auth 0],
BI [auth 0],
BJ [auth 0],
BK [auth 0],
CH [auth 0],
CI [auth 0],
CJ [auth 0],
DH [auth 0],
DI [auth 0],
DJ [auth 0],
DL [auth R],
EH [auth 0],
EI [auth 0],
EJ [auth 0],
FH [auth 0],
FI [auth 0],
FJ [auth 0],
FK [auth A],
FL [auth S],
GH [auth 0],
GI [auth 0],
GJ [auth 0],
GK [auth A],
HH [auth 0],
HI [auth 0],
HJ [auth 0],
IH [auth 0],
II [auth 0],
IJ [auth 0],
JH [auth 0],
JI [auth 0],
JJ [auth 0],
JK [auth B],
KH [auth 0],
KI [auth 0],
KJ [auth 0],
KK [auth B],
LG [auth 0],
LH [auth 0],
LI [auth 0],
LJ [auth 0],
MG [auth 0],
MH [auth 0],
MI [auth 0],
MJ [auth 0],
MK [auth F],
ML [auth 1],
NG [auth 0],
NH [auth 0],
NI [auth 0],
NJ [auth 0],
OG [auth 0],
OH [auth 0],
OI [auth 0],
OJ [auth 0],
PG [auth 0],
PH [auth 0],
PI [auth 0],
PJ [auth 0],
QG [auth 0],
QH [auth 0],
QI [auth 0],
QJ [auth 0],
QL [auth 3],
RG [auth 0],
RH [auth 0],
RI [auth 0],
RJ [auth 0],
RL [auth 3],
SG [auth 0],
SH [auth 0],
SI [auth 0],
SJ [auth 0],
TG [auth 0],
TH [auth 0],
TI [auth 0],
TJ [auth 0],
UG [auth 0],
UH [auth 0],
UI [auth 0],
UJ [auth 0],
VG [auth 0],
VH [auth 0],
VI [auth 0],
VJ [auth 0],
WG [auth 0],
WH [auth 0],
WI [auth 0],
WJ [auth 0],
WL [auth 9],
XG [auth 0],
XH [auth 0],
XI [auth 0],
XJ [auth 0],
XL [auth 9],
YG [auth 0],
YH [auth 0],
YI [auth 0],
YJ [auth 0],
YL [auth 9],
ZG [auth 0],
ZH [auth 0],
ZI [auth 0],
ZJ [auth 0]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
K
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MD [auth 0],
ND [auth 0]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
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CG [auth 0]
CL [auth R]
DG [auth 0]
EG [auth 0]
EK [auth A]
CG [auth 0],
CL [auth R],
DG [auth 0],
EG [auth 0],
EK [auth A],
FG [auth 0],
GG [auth 0],
HG [auth 0],
IG [auth 0],
IK [auth B],
JG [auth 0],
JL [auth Y],
KG [auth 0],
PK [auth J],
PL [auth 3],
QK [auth J],
RK [auth J],
TK [auth K],
UK [auth L],
WK [auth M],
XK [auth N],
ZK [auth O]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
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AB [auth 0]
AC [auth 0]
AD [auth 0]
BB [auth 0]
BC [auth 0]
AB [auth 0],
AC [auth 0],
AD [auth 0],
BB [auth 0],
BC [auth 0],
BD [auth 0],
CB [auth 0],
CC [auth 0],
CD [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DK [auth A],
EB [auth 0],
EC [auth 0],
ED [auth 0],
FA [auth 0],
FB [auth 0],
FC [auth 0],
FD [auth 0],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
GL [auth T],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HD [auth 0],
HK [auth B],
IA [auth 0],
IB [auth 0],
IC [auth 0],
ID [auth 0],
IL [auth Y],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JD [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],
NA [auth 0],
NB [auth 0],
NC [auth 0],
NL [auth 2],
OA [auth 0],
OB [auth 0],
OC [auth 0],
PA [auth 0],
PB [auth 0],
PC [auth 0],
QA [auth 0],
QB [auth 0],
QC [auth 0],
RA [auth 0],
RB [auth 0],
RC [auth 0],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SK [auth K],
SL [auth 9],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TL [auth 9],
UA [auth 0],
UB [auth 0],
UC [auth 0],
VA [auth 0],
VB [auth 0],
VC [auth 0],
WA [auth 0],
WB [auth 0],
WC [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
YA [auth 0],
YB [auth 0],
YC [auth 0],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
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AE [auth 0]
AF [auth 0]
AG [auth 0]
AL [auth Q]
BE [auth 0]
AE [auth 0],
AF [auth 0],
AG [auth 0],
AL [auth Q],
BE [auth 0],
BF [auth 0],
BG [auth 0],
BL [auth R],
CE [auth 0],
CF [auth 0],
DE [auth 0],
DF [auth 0],
EE [auth 0],
EF [auth 0],
EL [auth S],
FE [auth 0],
FF [auth 0],
GE [auth 0],
GF [auth 0],
HE [auth 0],
HF [auth 0],
IE [auth 0],
IF [auth 0],
JE [auth 0],
JF [auth 0],
KE [auth 0],
KF [auth 0],
LE [auth 0],
LF [auth 0],
LK [auth C],
ME [auth 0],
MF [auth 0],
NE [auth 0],
NF [auth 0],
NK [auth H],
OD [auth 0],
OE [auth 0],
OF [auth 0],
OK [auth J],
PD [auth 0],
PE [auth 0],
PF [auth 0],
QD [auth 0],
QE [auth 0],
QF [auth 0],
RD [auth 0],
RE [auth 0],
RF [auth 0],
SD [auth 0],
SE [auth 0],
SF [auth 0],
TD [auth 0],
TE [auth 0],
TF [auth 0],
UD [auth 0],
UE [auth 0],
UF [auth 0],
UL [auth 9],
VD [auth 0],
VE [auth 0],
VF [auth 0],
VK [auth M],
VL [auth 9],
WD [auth 0],
WE [auth 0],
WF [auth 0],
XD [auth 0],
XE [auth 0],
XF [auth 0],
YD [auth 0],
YE [auth 0],
YF [auth 0],
ZD [auth 0],
ZE [auth 0],
ZF [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.207α = 90
b = 299.544β = 90
c = 574.251γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2015-03-18
    Changes: Structure summary
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary