4ZER

Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex.

Seefeldt, A.C.Nguyen, F.Antunes, S.Perebaskine, N.Graf, M.Arenz, S.Inampudi, K.K.Douat, C.Guichard, G.Wilson, D.N.Innis, C.A.

(2015) Nat Struct Mol Biol 22: 470-475

  • DOI: 10.1038/nsmb.3034
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The increasing prevalence of multidrug-resistant pathogenic bacteria is making current antibiotics obsolete. Proline-rich antimicrobial peptides (PrAMPs) display potent activity against Gram-negative bacteria and thus represent an avenue for antibiot ...

    The increasing prevalence of multidrug-resistant pathogenic bacteria is making current antibiotics obsolete. Proline-rich antimicrobial peptides (PrAMPs) display potent activity against Gram-negative bacteria and thus represent an avenue for antibiotic development. PrAMPs from the oncocin family interact with the ribosome to inhibit translation, but their mode of action has remained unclear. Here we have determined a structure of the Onc112 peptide in complex with the Thermus thermophilus 70S ribosome at a resolution of 3.1 Å by X-ray crystallography. The Onc112 peptide binds within the ribosomal exit tunnel and extends toward the peptidyl transferase center, where it overlaps with the binding site for an aminoacyl-tRNA. We show biochemically that the binding of Onc112 blocks and destabilizes the initiation complex, thus preventing entry into the elongation phase. Our findings provide a basis for the future development of this class of potent antimicrobial agents.


    Organizational Affiliation

    1] Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. [2] INSERM U869, Bordeaux, France.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
1D, 2D
275Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
1E, 2E
204Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
1F, 2F
203Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
1G, 2G
181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
1H, 2H
174Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
1I, 2I
147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
1N, 2N
140Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
1O, 2O
122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
1P, 2P
149Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
1Q, 2Q
141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
1R, 2R
118Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
1S, 2S
110Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
1T, 2T
131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
1U, 2U
116Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
1V, 2V
101Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
1W, 2W
112Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
1X, 2X
95Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
1Y, 2Y
107Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z, 2Z
203Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
10, 20
77Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
11, 21
97Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
12, 22
70Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13, 23
59Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
14, 24
69Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
15, 25
59Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
16, 26
53Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
17, 27
48Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
18, 28
64Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
19, 29
37Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I28

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1b, 2b
231Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
1c, 2c
206Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
1d, 2d
208Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
1e, 2e
148Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
1f, 2f
100Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
1g, 2g
155Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
1h, 2h
137Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
1i, 2i
127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1j, 2j
97Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k, 2k
114Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l, 2l
122Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m, 2m
116Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
1n, 2n
60Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o, 2o
88Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p, 2p
82Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
1q, 2q
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1r, 2r
68Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
1s, 2s
83Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
1t, 2t
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
1u, 2u
23Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Onc112
1y, 2y
19Oncopeltus fasciatusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 1
MoleculeChainsLengthOrganism
23s ribosomal RNA1A, 2A2915Thermus thermophilus HB8

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Entity ID: 2
MoleculeChainsLengthOrganism
5s ribosomal RNA1B, 2B120Thermus thermophilus HB8

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Entity ID: 32
MoleculeChainsLengthOrganism
16s ribosomal RNA1a, 2a1521Thermus thermophilus HB8

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Entity ID: 53
MoleculeChainsLengthOrganism
tRNA met1x, 2x76Escherichia coli K-12

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Entity ID: 55
MoleculeChainsLengthOrganism
mRNAA, B27Thermus thermophilus HB8
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ARG
Query on ARG

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1B
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
MPD
Query on MPD

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1A, 1a
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

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14, 15, 16, 19, 1Y, 1n, 24, 25, 26, 29, 2Y, 2n
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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2A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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10, 11, 13, 15, 17, 18, 19, 1A, 1B, 1D, 1E, 1F, 1G, 1H, 1N, 1O, 1P, 1Q, 1R, 1T, 1U, 1V, 1W, 1X, 1Y, 1Z, 1a, 1b, 1d, 1e, 1f, 1g, 1i, 1l, 1n, 1o, 1r, 1t, 1x, 20, 21, 23, 28, 2A, 2B, 2D, 2E, 2F, 2G, 2I, 2N, 2O, 2P, 2Q, 2R, 2T, 2U, 2V, 2W, 2X, 2Y, 2a, 2e, 2f, 2j, 2k, 2l, 2n, 2p, 2q, 2t, 2x
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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1A, 2A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
1l,2l
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.3α = 90
b = 452.29β = 90
c = 625.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-06-03
    Changes: Database references
  • Version 1.2: 2015-06-10
    Changes: Database references
  • Version 1.3: 2016-01-13
    Changes: Structure summary
  • Version 1.4: 2016-03-23
    Changes: Structure summary
  • Version 1.5: 2017-10-18
    Changes: Data collection