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Crystal structure of the E. coli ribosome bound to CEM-101


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.

Llano-Sotelo, B.Dunkle, J.Klepacki, D.Zhang, W.Fernandes, P.Cate, J.H.Mankin, A.S.

(2010) Antimicrob. Agents Chemother. 54: 4961-4970

  • DOI: 10.1128/AAC.00860-10
  • Primary Citation of Related Structures:  1VT2, 3OR9, 3ORA, 3ORB, 4V80

  • PubMed Abstract: 
  • We characterized the mechanism of action and the drug-binding site of a novel ketolide, CEM-101, which belongs to the latest class of macrolide antibiotics. CEM-101 shows high affinity for the ribosomes of Gram-negative (Escherichia coli) and Gram-po ...

    We characterized the mechanism of action and the drug-binding site of a novel ketolide, CEM-101, which belongs to the latest class of macrolide antibiotics. CEM-101 shows high affinity for the ribosomes of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. The ketolide shows high selectivity in its inhibitory action and readily interferes with synthesis of a reporter protein in the bacterial but not eukaryotic cell-free translation system. Binding of CEM-101 to its ribosomal target site was characterized biochemically and by X-ray crystallography. The X-ray structure of CEM-101 in complex with the E. coli ribosome shows that the drug binds in the major macrolide site in the upper part of the ribosomal exit tunnel. The lactone ring of the drug forms hydrophobic interactions with the walls of the tunnel, the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft, and the extended alkyl-aryl arm of the drug is oriented down the tunnel and makes contact with a base pair formed by A752 and U2609 of the 23S rRNA. The position of the CEM-101 alkyl-aryl extended arm differs from that reported for the side chain of the ketolide telithromycin complexed with either bacterial (Deinococcus radiodurans) or archaeal (Haloarcula marismortui) large ribosomal subunits but closely matches the position of the side chain of telithromycin complexed to the E. coli ribosome. A difference in the chemical structure of the side chain of CEM-101 in comparison with the side chain of telithromycin and the presence of the fluorine atom at position 2 of the lactone ring likely account for the superior activity of CEM-101. The results of chemical probing suggest that the orientation of the CEM-101 extended side chain observed in the E. coli ribosome closely resembles its placement in Staphylococcus aureus ribosomes and thus likely accurately reflects interaction of CEM-101 with the ribosomes of the pathogenic bacterial targets of the drug. Chemical probing further demonstrated weak binding of CEM-101, but not of erythromycin, to the ribosome dimethylated at A2058 by the action of Erm methyltransferase.


    Organizational Affiliation

    Center for Pharmaceutical Biotechnology-m/c 870, University of Illinois, 900 S. Ashland Ave., Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
RC, YC
271Escherichia coli (strain K12)Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
RD, YD
209Escherichia coli (strain K12)Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
RE, YE
201Escherichia coli (strain K12)Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
RF, YF
178Escherichia coli (strain K12)Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
RG, YG
176Escherichia coli (strain K12)Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
RH, YH
149Escherichia coli (strain K12)Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
RI, YI
141Escherichia coli (strain K12)Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
RJ, YJ
142Escherichia coli (strain K12)Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
RK, YK
122Escherichia coli (strain K12)Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
RL, YL
143Escherichia coli (strain K12)Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
RM, YM
136Escherichia coli (strain K12)Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
RN, YN
120Escherichia coli (strain K12)Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
RO, YO
116Escherichia coli (strain K12)Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
RP, YP
114Escherichia coli (strain K12)Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
RQ, YQ
117Escherichia coli (strain K12)Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
RR, YR
103Escherichia coli (strain K12)Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
RS, YS
110Escherichia coli (strain K12)Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
RT, YT
93Escherichia coli (strain K12)Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
RU, YU
102Escherichia coli (strain K12)Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
RV, YV
94Escherichia coli (strain K12)Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
RW, YW
79Escherichia coli (strain K12)Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
RX, YX
77Escherichia coli (strain K12)Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
RY, YY
63Escherichia coli (strain K12)Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
RZ, YZ
58Escherichia coli (strain K12)Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
R0, Y0
56Escherichia coli (strain K12)Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
R1, Y1
50Escherichia coli (strain K12)Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
R2, Y2
46Escherichia coli (strain K12)Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
R3, Y3
64Escherichia coli (strain K12)Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
R4, Y4
38Escherichia coli (strain K12)Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
QB, XB
218Escherichia coli (strain K12)Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
QC, XC
206Escherichia coli (strain K12)Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
QD, XD
205Escherichia coli (strain K12)Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
QE, XE
150Escherichia coli (strain K12)Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
QF, XF
100Escherichia coli (strain K12)Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
QG, XG
151Escherichia coli (strain K12)Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
QH, XH
129Escherichia coli (strain K12)Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
QI, XI
127Escherichia coli (strain K12)Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
QJ, XJ
98Escherichia coli (strain K12)Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
QK, XK
117Escherichia coli (strain K12)Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
QL, XL
123Escherichia coli (strain K12)Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
QM, XM
114Escherichia coli (strain K12)Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
QN, XN
101Escherichia coli (strain K12)Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
QO, XO
88Escherichia coli (strain K12)Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
QP, XP
82Escherichia coli (strain K12)Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
QQ, XQ
80Escherichia coli (strain K12)Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
QR, XR
55Escherichia coli (strain K12)Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
QS, XS
79Escherichia coli (strain K12)Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
QT, XT
85Escherichia coli (strain K12)Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
QU, XU
51Escherichia coli (strain K12)Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNARA,YA2904Escherichia coli str. K-12 substr. MG1655
Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNARB,YB118Escherichia coli str. K-12 substr. MG1655
Entity ID: 32
MoleculeChainsLengthOrganism
16S rRNAQA,XA1533Escherichia coli str. K-12 substr. MG1655
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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R4, Y4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EM1
Query on EM1

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RA
(3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
CEM-101
C43 H65 F N6 O10
IXXFZUPTQVDPPK-ZAWHAJPISA-N
 Ligand Interaction
MG
Query on MG

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QA, RA, RB, XA, YA, YB, YE, YJ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 210.759α = 90.00
b = 433.272β = 90.00
c = 618.863γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release