5F8K

Crystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.

Seefeldt, A.C.Graf, M.Perebaskine, N.Nguyen, F.Arenz, S.Mardirossian, M.Scocchi, M.Wilson, D.N.Innis, C.A.

(2016) Nucleic Acids Res 44: 2429-2438

  • DOI: 10.1093/nar/gkv1545
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Proline-rich antimicrobial peptides (PrAMPs) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. PrAMPs such as oncocin or ba ...

    Proline-rich antimicrobial peptides (PrAMPs) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. PrAMPs such as oncocin or bactenecin-7 (Bac7) interact with the bacterial ribosome to inhibit translation, but their supposed specificity as inhibitors of bacterial rather than mammalian protein synthesis remains unclear, despite being key to developing drugs with low toxicity. Here, we present crystal structures of the Thermus thermophilus 70S ribosome in complex with the first 16 residues of mammalian Bac7, as well as the insect-derived PrAMPs metalnikowin I and pyrrhocoricin. The structures reveal that the mammalian Bac7 interacts with a similar region of the ribosome as insect-derived PrAMPs. Consistently, Bac7 and the oncocin derivative Onc112 compete effectively with antibiotics, such as erythromycin, which target the ribosomal exit tunnel. Moreover, we demonstrate that Bac7 allows initiation complex formation but prevents entry into the elongation phase of translation, and show that it inhibits translation on both mammalian and bacterial ribosomes, explaining why this peptide needs to be stored as an inactive pro-peptide. These findings highlight the need to consider the specificity of PrAMP derivatives for the bacterial ribosome in future drug development efforts.


    Organizational Affiliation

    Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France U1212, Inserm, Bordeaux 33076, France UMR 5320, CNRS, Bordeaux 33076, France axel.innis@inserm.fr.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31E, 2E204Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L41F, 2F203Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L51G, 2G181Thermus 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 L61H, 2H174Thermus thermophilus HB8Mutation(s): 0 
Find proteins for A0A0M9ADP1 (Thermus aquaticus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L91I, 2I147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L131N, 2N140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L141O, 2O122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L151P, 2P149Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L161Q, 2Q141Thermus 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 L171R, 2R118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L191T, 2T131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L201U, 2U116Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L211V, 2V101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L221W, 2W112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L241Y, 2Y107Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L251Z, 2Z203Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2710, 2077Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2811, 2197Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2912, 2270Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3013, 2359Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3114, 2469Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3215, 2559Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3316, 2653Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3417, 2748Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3518, 2864Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3619, 2937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21b, 2b231Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S31c, 2c206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S61f, 2f100Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S71g, 2g155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S81h, 2h137Thermus thermophilus HB8Mutation(s): 0 
Find proteins for A0A0M9AFS9 (Thermus aquaticus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S91i, 2i127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S111k, 2k114Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S121l, 2l122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S131m, 2m116Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z1n, 2n60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S151o, 2o88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S161p, 2p82Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S171q, 2q99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S181r, 2r68Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S191s, 2s83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S201t, 2t98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L181S, 2S110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L231X, 2X95Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21D, 2D275Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S41d, 2d208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S51e, 2e148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S101j, 2j97Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx1u, 2u23Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Cathelicidin-31y, 2y16Bos taurusMutation(s): 0 
Gene Names: CATHL3BAC7
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  • Reference Sequence

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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, 2a1520Thermus thermophilus HB8

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Entity ID: 54
MoleculeChainsLengthOrganism
tRNAiMet1x, 2x76Escherichia coli K-12
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Entity ID: 53
MoleculeChainsLengthOrganism
mRNA1v, 2v3synthetic construct
Small Molecules
Ligands 4 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
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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1x, 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, 1P, 1Q, 1R, 1S, 1T, 1U, 1V, 1W, 1X, 1a, 1b, 1d, 1e, 1f, 1g, 1h, 1i, 1l, 1n, 1o, 1q, 1t, 1x, 20, 23, 25, 27, 28, 29, 2A, 2B, 2D, 2E, 2F, 2G, 2H, 2N, 2P, 2Q, 2R, 2S, 2U, 2V, 2W, 2X, 2Y, 2a, 2b, 2d, 2e, 2f, 2g, 2h, 2i, 2j, 2l, 2n, 2o, 2t, 2v, 2x
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
1l,2lL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.96α = 90
b = 450.13β = 90
c = 622.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Structure summary
  • Version 1.2: 2016-03-30
    Changes: Database references