3J9Y

Cryo-EM structure of tetracycline resistance protein TetM bound to a translating E.coli ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Cryo-EM structure of the tetracycline resistance protein TetM in complex with a translating ribosome at 3.9- angstrom resolution.

Arenz, S.Nguyen, F.Beckmann, R.Wilson, D.N.

(2015) Proc Natl Acad Sci U S A 112: 5401-5406

  • DOI: 10.1073/pnas.1501775112
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosome protection proteins (RPPs) confer resistance to tetracycline by binding to the ribosome and chasing the drug from its binding site. Current models for RPP action are derived from 7.2- to 16-Å resolution structures of RPPs bound to vacant or ...

    Ribosome protection proteins (RPPs) confer resistance to tetracycline by binding to the ribosome and chasing the drug from its binding site. Current models for RPP action are derived from 7.2- to 16-Å resolution structures of RPPs bound to vacant or nontranslating ribosomes. Here we present a cryo-electron microscopy reconstruction of the RPP TetM in complex with a translating ribosome at 3.9-Å resolution. The structure reveals the contacts of TetM with the ribosome, including interaction between the conserved and functionally critical C-terminal extension of TetM with a unique splayed conformation of nucleotides A1492 and A1493 at the decoding center of the small subunit. The resolution enables us to unambiguously model the side chains of the amino acid residues comprising loop III in domain IV of TetM, revealing that the tyrosine residues Y506 and Y507 are not responsible for drug-release as suggested previously but rather for intrafactor contacts that appear to stabilize the conformation of loop III. Instead, Pro509 at the tip of loop III is located directly within the tetracycline binding site where it interacts with nucleotide C1054 of the 16S rRNA, such that RPP action uses Pro509, rather than Y506/Y507, to directly dislodge and release tetracycline from the ribosome.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany; and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany wilson@genzentrum.lmu.de.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
82Escherichia coliMutation(s): 0 
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
84Escherichia coliMutation(s): 0 
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
75Escherichia coliMutation(s): 0 
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
87Escherichia coliMutation(s): 0 
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
71Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Tetracycline resistance protein TetM
w
639Enterococcus faecalisMutation(s): 0 
Gene Names: tetMtet(M)
Find proteins for P21598 (Enterococcus faecalis)
Go to UniProtKB:  P21598
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
233Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
179Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
240Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
130Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
103Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
118Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
102Escherichia coliMutation(s): 0 
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
92Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
206Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
167Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
78Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
135Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
57Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
55Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
65Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
5
165Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
70Escherichia coliMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
7
69Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
130Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
129Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Escherichia coliMutation(s): 0 
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1539Escherichia coli

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Entity ID: 15
MoleculeChainsLengthOrganism
P-site fMet-tRNAfMetv78Escherichia coli
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Entity ID: 16
MoleculeChainsLengthOrganism
mRNAx11Escherichia coli

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Entity ID: 25
MoleculeChainsLengthOrganism
23S ribosomal RNAA2903Escherichia coli

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Entity ID: 26
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
vL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2015-05-13
    Changes: Database references
  • Version 2.0: 2018-07-18
    Changes: Data collection, Polymer sequence