1YIT

Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

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This is version 2.1 of the entry. See complete history


Literature

Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance.

TU, D.Blaha, G.Moore, P.B.Steitz, T.A.

(2005) Cell 121: 257

  • DOI: https://doi.org/10.1016/j.cell.2005.02.005
  • Primary Citation of Related Structures:  
    1YHQ, 1YI2, 1YIJ, 1YIT, 1YJ9, 1YJN, 1YJW

  • PubMed Abstract: 

    Crystal structures of H. marismortui large ribosomal subunits containing the mutation G2099A (A2058 in E. coli) with erythromycin, azithromycin, clindamycin, virginiamycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are resistant to them. Azithromycin binds almost identically to both G2099A and wild-type subunits, but the erythromycin affinity increases by more than 10(4)-fold, implying that desolvation of the N2 of G2099 accounts for the low wild-type affinity for macrolides. All macrolides bind similarly to the H. marismortui subunit, but their binding differs significantly from what has been reported in the D. radioidurans subunit. The synergy in the binding of streptogramins A and B appears to result from a reorientation of the base of A2103 (A2062, E. coli) that stacks between them. The structure of large subunit containing a three residue deletion mutant of L22 shows a change in the L22 structure and exit tunnel shape that illuminates its macrolide resistance phenotype.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L37EB [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (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 L39EC [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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L44ED [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VIRGINIAMYCIN S1E [auth 8]7Streptomyces virginiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2PG [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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3PH [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4EI [auth C]246Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5PJ [auth D]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6PK [auth E]178Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AEL [auth F]120Haloarcula marismortuiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOGM [auth G]348Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EN [auth H]177Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11PO [auth I]162Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13PP [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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14PQ [auth K]132Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15PR [auth L]165Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12737 (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 L15ES [auth M]195Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18PT [auth N]187Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18EU [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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19EV [auth P]149Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (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 L21EW [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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22PX [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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23PY [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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24PZ [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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24EAA [auth U]66Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29PBA [auth V]71Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30PCA [auth W]154Haloarcula marismortuiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31EDA [auth X]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32EEA [auth Y]241Haloarcula marismortuiMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L37AEFA [auth Z]83Haloarcula 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: 6
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAF [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VIR
Query on VIR

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RH [auth 0]VIRGINIAMYCIN M1
C28 H35 N3 O7
DAIKHDNSXMZDCU-FQTGFAPKSA-N
CD
Query on CD

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AJ [auth U],
DJ [auth Z],
SH [auth 1],
SI [auth O],
VH [auth 3]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

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

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CI [auth A]
CJ [auth Y]
FI [auth B]
HH [auth 0]
IH [auth 0]
CI [auth A],
CJ [auth Y],
FI [auth B],
HH [auth 0],
IH [auth 0],
JH [auth 0],
JI [auth J],
KH [auth 0],
KI [auth J],
LH [auth 0],
LI [auth J],
MH [auth 0],
NH [auth 0],
OH [auth 0],
OI [auth L],
PH [auth 0],
QH [auth 0],
QI [auth M],
RI [auth N],
TI [auth O],
WH [auth 3],
XI [auth R]
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]
AI [auth A]
AB [auth 0],
AC [auth 0],
AD [auth 0],
AE [auth 0],
AI [auth A],
BB [auth 0],
BC [auth 0],
BD [auth 0],
BE [auth 0],
BJ [auth Y],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
DI [auth B],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
EI [auth B],
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],
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],
KE [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],
MI [auth K],
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],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TD [auth 0],
TH [auth 2],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UD [auth 0],
UH [auth 3],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
XH [auth 9],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0],
ZI [auth T]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AF [auth 0]
AG [auth 0]
AH [auth 0]
BF [auth 0]
BG [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth A],
CF [auth 0],
CG [auth 0],
CH [auth 0],
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],
GI [auth C],
HF [auth 0],
HG [auth 0],
HI [auth H],
IF [auth 0],
IG [auth 0],
II [auth J],
JF [auth 0],
JG [auth 0],
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],
NI [auth L],
OE [auth 0],
OF [auth 0],
OG [auth 0],
PE [auth 0],
PF [auth 0],
PG [auth 0],
PI [auth M],
QE [auth 0],
QF [auth 0],
QG [auth 0],
RE [auth 0],
RF [auth 0],
RG [auth 0],
SE [auth 0],
SF [auth 0],
SG [auth 0],
TE [auth 0],
TF [auth 0],
TG [auth 0],
UE [auth 0],
UF [auth 0],
UG [auth 0],
UI [auth Q],
VE [auth 0],
VF [auth 0],
VG [auth 0],
VI [auth R],
WE [auth 0],
WF [auth 0],
WG [auth 0],
WI [auth R],
XE [auth 0],
XF [auth 0],
XG [auth 0],
YE [auth 0],
YF [auth 0],
YG [auth 0],
YH [auth 9],
YI [auth S],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0],
ZH [auth 9]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
E [auth 8]L-PEPTIDE LINKINGC10 H13 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.583α = 90
b = 299.758β = 90
c = 573.56γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata 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: 2005-04-26
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 2.0: 2024-07-10
    Changes: Data collection, Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2024-10-09
    Changes: Structure summary