3J5L

Structure of the E. coli 50S subunit with ErmBL nascent chain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.

Arenz, S.Ramu, H.Gupta, P.Berninghausen, O.Beckmann, R.Vazquez-Laslop, N.Mankin, A.S.Wilson, D.N.

(2014) Nat Commun 5: 3501-3501

  • DOI: 10.1038/ncomms4501
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In bacteria, ribosome stalling during translation of ErmBL leader peptide occurs in the presence of the antibiotic erythromycin and leads to induction of expression of the downstream macrolide resistance methyltransferase ErmB. The lack of structures ...

    In bacteria, ribosome stalling during translation of ErmBL leader peptide occurs in the presence of the antibiotic erythromycin and leads to induction of expression of the downstream macrolide resistance methyltransferase ErmB. The lack of structures of drug-dependent stalled ribosome complexes (SRCs) has limited our mechanistic understanding of this regulatory process. Here we present a cryo-electron microscopy structure of the erythromycin-dependent ErmBL-SRC. The structure reveals that the antibiotic does not interact directly with ErmBL, but rather redirects the path of the peptide within the tunnel. Furthermore, we identify a key peptide-ribosome interaction that defines an important relay pathway from the ribosomal tunnel to the peptidyltransferase centre (PTC). The PTC of the ErmBL-SRC appears to adopt an uninduced state that prevents accommodation of Lys-tRNA at the A-site, thus providing structural basis for understanding how the drug and the nascent peptide cooperate to inhibit peptide bond formation and induce translation arrest.


    Organizational Affiliation

    1] Gene Center, Department for Biochemistry, University of Munich, Feodor-Lynen Strasse 25, 81377 Munich, Germany [2] Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynen Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Erythromycin resistance leader peptide
6
10Streptococcus sanguinisMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
56Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
50Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
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Entity ID: 9
MoleculeChainsLengthOrganism
23S ribsomal RNAA2904Escherichia coli K-12

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Entity ID: 10
MoleculeChainsLengthOrganism
5S ribosomal RNAB118Escherichia coli K-12
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Entity ID: 6
MoleculeChainsLengthOrganism
5'-R(*CP*(MA6))-3'52N/A
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Entity ID: 8
MoleculeChainsLengthOrganism
5'-R(*CP*CP*A)-3'73N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERY
Query on ERY

Download CCD File 
A
ERYTHROMYCIN A
C37 H67 N O13
ULGZDMOVFRHVEP-RWJQBGPGSA-N
 Ligand Interaction
UNL
Query on UNL

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5
Unknown ligand
ULGZDMOVFRHVEP-RWJQBGPGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection