5NRG

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with RB02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.442 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.

Matzov, D.Eyal, Z.Benhamou, R.I.Shalev-Benami, M.Halfon, Y.Krupkin, M.Zimmerman, E.Rozenberg, H.Bashan, A.Fridman, M.Yonath, A.

(2017) Nucleic Acids Res. 45: 10284-10292

  • DOI: 10.1093/nar/gkx658
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus ...

    Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen. This small, albeit important group of antibiotics is mostly active against Gram-positive bacteria, but also used against selected Gram-negative anaerobes and protozoa. S. aureus resistance to lincosamides can be acquired by modifications and/or mutations in the rRNA and rProteins. Here, we present the crystal structures of the large ribosomal subunit of S. aureus in complex with the lincosamides lincomycin and RB02, a novel semisynthetic derivative and discuss the biochemical aspects of the in vitro potency of various lincosamides. These results allow better understanding of the drugs selectivity as well as the importance of the various chemical moieties of the drug for binding and inhibition.


    Organizational Affiliation

    Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
A
277Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
B
220Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
C
207Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
D
179Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW18
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
E
178Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW21
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
G
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
H
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
I
140Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplO
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
J
144Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
K
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
L
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
M
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
N
118Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
O
102Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
P
117Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
Q
91Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
R
105Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
S
217Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0S0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
T
94Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
V
69Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
W
59Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Z
58Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmF
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZF1
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
45Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
66Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAX2923Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAY114Staphylococcus aureus subsp. aureus NCTC 8325
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
X
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
3, E, I, X, Y, Z
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
3, C, G, J, X, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
95H
Query on 95H

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Download CCD File 
X
~{N}-[(1~{R},2~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-methylsulfanyl-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanyl-propyl]-4-nitro-benzamide
RB02
C16 H22 N2 O8 S
KAMQPAUJKUPLQE-CVTPPLIDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
X
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SPD
Query on SPD

Download SDF File 
Download CCD File 
X
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.442 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 279.797α = 90.00
b = 279.797β = 90.00
c = 873.274γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references