5O2R

Cryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.

Florin, T.Maracci, C.Graf, M.Karki, P.Klepacki, D.Berninghausen, O.Beckmann, R.Vazquez-Laslop, N.Wilson, D.N.Rodnina, M.V.Mankin, A.S.

(2017) Nat Struct Mol Biol 24: 752-757

  • DOI: 10.1038/nsmb.3439
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of m ...

    Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation. Here we show that Api137, a derivative of the insect-produced antimicrobial peptide apidaecin, arrests terminating ribosomes using a unique mechanism of action. Api137 binds to the Escherichia coli ribosome and traps release factor (RF) RF1 or RF2 subsequent to the release of the nascent polypeptide chain. A high-resolution cryo-EM structure of the ribosome complexed with RF1 and Api137 reveals the molecular interactions that lead to RF trapping. Api137-mediated depletion of the cellular pool of free release factors causes the majority of ribosomes to stall at stop codons before polypeptide release, thereby resulting in a global shutdown of translation termination.


    Organizational Affiliation

    Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 6
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: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
50Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
66Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
157Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
Find proteins for P0A7S9 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor RF1
v
242Escherichia coli K-12Mutation(s): 0 
Gene Names: prfAsueBuarb1211JW1202
Find proteins for P0A7I0 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Apidaecin
z
14Apis melliferaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
5
131Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
116Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA2903Escherichia coli K-12
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Entity ID: 34
MoleculeChainsLengthOrganism
mRNA77Staphylococcus aureus

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Entity ID: 57
MoleculeChainsLengthOrganism
P-site Ile-tRNAx77Escherichia coli K-12

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli K-12

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Entity ID: 35
MoleculeChainsLengthOrganism
16S ribosomal RNAa1539Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
iNEXTCzech RepublicProject 2259
German Research FoundationGermanyFOR1805

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations