5FDV image
Deposition Date 2015-12-16
Release Date 2016-01-27
Last Version Date 2025-03-12
Entry Detail
PDB ID:
5FDV
Keywords:
Title:
Crystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus thermophilus 70S ribosome
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: 10), YB (auth: 20)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: 11), ZB (auth: 21)
Chain Length:97
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: 12), AC (auth: 22)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: 13), BC (auth: 23)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: 14), CC (auth: 24)
Chain Length:69
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 15), DC (auth: 25)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 16), EC (auth: 26)
Chain Length:53
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 17), FC (auth: 27)
Chain Length:48
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 18), GC (auth: 28)
Chain Length:64
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 19), HC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: 1A), DB (auth: 2A)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 1B), EB (auth: 2B)
Chain Length:231
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: 1D), FB (auth: 2D)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: 1E), GB (auth: 2E)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: 1F), HB (auth: 2F)
Chain Length:203
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: 1G), IB (auth: 2G)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:G (auth: 1H), JB (auth: 2H)
Chain Length:174
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: 1I), KB (auth: 2I)
Chain Length:147
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: 1N), LB (auth: 2N)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: 1O), MB (auth: 2O)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: 1P), NB (auth: 2P)
Chain Length:82
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: 1Q), OB (auth: 2Q)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: 1R), PB (auth: 2R)
Chain Length:68
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: 1S), QB (auth: 2S)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: 1T), RB (auth: 2T)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: 1U), SB (auth: 2U)
Chain Length:116
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: 1V), TB (auth: 2V)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: 1W), UB (auth: 2W)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: 1X), VB (auth: 2X)
Chain Length:95
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: 1Y), WB (auth: 2Y)
Chain Length:16
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: 1Z), XB (auth: 2Z)
Chain Length:203
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:FA (auth: 1a), IC (auth: 2a)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:HA (auth: 1b), JC (auth: 2b)
Chain Length:231
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:IA (auth: 1c), KC (auth: 2c)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:JA (auth: 1d), LC (auth: 2d)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:KA (auth: 1e), MC (auth: 2e)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:LA (auth: 1f), NC (auth: 2f)
Chain Length:203
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:MA (auth: 1g), OC (auth: 2g)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:NA (auth: 1h), PC (auth: 2h)
Chain Length:174
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:OA (auth: 1i), QC (auth: 2i)
Chain Length:147
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:PA (auth: 1j), RC (auth: 2j)
Chain Length:97
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:QA (auth: 1k), SC (auth: 2k)
Chain Length:114
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:RA (auth: 1l), TC (auth: 2l)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:SA (auth: 1m), UC (auth: 2m)
Chain Length:116
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:TA (auth: 1n), VC (auth: 2n)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:UA (auth: 1o), WC (auth: 2o)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:VA (auth: 1p), XC (auth: 2p)
Chain Length:82
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:WA (auth: 1q), YC (auth: 2q)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:XA (auth: 1r), ZC (auth: 2r)
Chain Length:68
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:YA (auth: 1s), AD (auth: 2s)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:ZA (auth: 1t), BD (auth: 2t)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:AB (auth: 1u), CD (auth: 2u)
Chain Length:116
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:Pyrrhocoricin
Chain IDs:CB (auth: 1y), DD (auth: 2y)
Chain Length:16
Number of Molecules:2
Biological Source:Pyrrhocoris apterus
Polymer Type:polypeptide(L)
Molecule:Ribosome-associated inhibitor A
Gene (Uniprot):raiA
Chain IDs:GA (auth: 2x), BB (auth: 1x)
Chain Length:95
Number of Molecules:2
Biological Source:Escherichia coli K-12
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD RA ASP modified residue
2MA A A modified residue
2MG FA G modified residue
4OC FA C modified residue
5MC A C modified residue
5MU A U modified residue
G7M FA G modified residue
M2G FA G modified residue
MA6 FA A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
UR3 FA U modified residue
Primary Citation
Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
Nucleic Acids Res. 44 2429 2438 (2016)
PMID: 26792896 DOI: 10.1093/nar/gkv1545

Abstact

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.

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Primary Citation of related structures