5KCS

Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Evernimycin, mRNA, TetM and P-site tRNA at 3.9A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome.

Arenz, S.Juette, M.F.Graf, M.Nguyen, F.Huter, P.Polikanov, Y.S.Blanchard, S.C.Wilson, D.N.

(2016) Proc.Natl.Acad.Sci.USA 113: 7527-7532

  • DOI: 10.1073/pnas.1604790113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ...

    The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
1D
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
1E
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
1F
201Escherichia coli (strain K12)Mutation(s): 0 
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
1G
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
1H
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
1L
121Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplL
Find proteins for P0A7K2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
1I
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
1J
165Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
1K
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
1N
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
1O
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
1P
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
1Q
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
1R
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
1S
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
1T
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
1U
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
1V
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
1W
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
1X
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
1Y
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
10
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
11
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
12
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
14
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
15
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
16
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
17
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
18
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
19
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1b
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
1c
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
1d
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
1e
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
1f
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
1g
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
1h
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
1i
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1j
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
1n
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o
89Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
1q
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1r
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
1s
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
1t
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
1u
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Tetracycline resistance protein TetM from transposon Tn916
1w
639Enterococcus faecalisMutation(s): 0 
Gene Names: tetM (tet(M))
Find proteins for P21598 (Enterococcus faecalis)
Go to UniProtKB:  P21598
Entity ID: 1
MoleculeChainsLengthOrganism
23S Ribosomal RNA1A2904Escherichia coli K-12
Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNA1B120Escherichia coli K-12
Entity ID: 35
MoleculeChainsLengthOrganism
16S Ribosomal RNA1a1539Escherichia coli K-12
Entity ID: 56
MoleculeChainsLengthOrganism
mRNA1v60synthetic construct
Entity ID: 58
MoleculeChainsLengthOrganism
P-site tRNA1x77Escherichia coli K-12
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EVN
Query on EVN

Download SDF File 
Download CCD File 
1A
(2R,3R,4R,6S)-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7S,7aR)-6-{[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5S,6S)-6-({(2R,3aS,3a'R,6S,7R,7'R,7aS,7a'S)-7'-[(2,4-dihydroxy-6-methylbenzoyl)oxy]-7-hydroxyoctahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}oxy)-4-hydroxy-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-3-hydroxy-5-methoxy-6-methyltetrahydro-2H-pyran-4-yl]oxy}-4',7-dihydroxy-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-4-{[(2R,4S,5R,6S)-5-methoxy-4,6-dim
Evernimicin
C70 H97 Cl2 N O38
UPADRKHAIMTUCC-LRNXXXSBSA-N
 Ligand Interaction
Modified Residues  17 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1a, 1A, 1x
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1A, 1a
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
1A
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
1A
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
1A
RNA LINKINGC11 H16 N5 O8 PG
OMC
Query on OMC
1A
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
1a
RNA LINKINGC12 H18 N5 O7 PA
2MG
Query on 2MG
1A, 1a
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
1A
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
1a
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
1A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
1a, 1x
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1A, 1x
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1A
RNA LINKINGC11 H16 N5 O7 PA
4OC
Query on 4OC
1a
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
1A
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
1A, 1x
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Illinois State Startup FundsUnited States--
German Research FoundationGermanyFOR1805
German Research FoundationGermanyWI3285/3-2
German Research FoundationGermanyGRK1721
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079238
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM098859

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Data collection
  • Version 2.0: 2018-07-18
    Type: Data collection, Polymer sequence