4ZER image
Deposition Date 2015-04-20
Release Date 2015-05-20
Last Version Date 2025-03-12
Entry Detail
PDB ID:
4ZER
Keywords:
RIBOSOME
Title:
Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
Oncopeltus fasciatus (Taxon ID: 7536)
Thermus thermophilus HB8 (Taxon ID: 300852)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.10 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
4ZER validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: 10), XB (auth: 20)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60493 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: 11), YB (auth: 21)
Chain Length:97
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60494 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:X (auth: 12), ZB (auth: 22)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Y (auth: 13), AC (auth: 23)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:Z (auth: 14), BC (auth: 24)
Chain Length:69
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJE1 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 15), CC (auth: 25)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80339 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:BA (auth: 16), DC (auth: 26)
Chain Length:53
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P35871 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 17), EC (auth: 27)
Chain Length:48
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:DA (auth: 18), FC (auth: 28)
Chain Length:64
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SKU1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:EA (auth: 19), GC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23s ribosomal RNA
Chain IDs:A (auth: 1A), CB (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), DB (auth: 2B)
Chain Length:120
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:C (auth: 1D), EB (auth: 2D)
Chain Length:275
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:D (auth: 1E), FB (auth: 2E)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN8 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: 1F), GB (auth: 2F)
Chain Length:203
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN9 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: 1G), HB (auth: 2G)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:G (auth: 1H), IB (auth: 2H)
Chain Length:174
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY8 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: 1I), JB (auth: 2I)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:I (auth: 1N), KB (auth: 2N)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60488 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: 1O), LB (auth: 2O)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:K (auth: 1P), MB (auth: 2P)
Chain Length:149
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: 1Q), NB (auth: 2Q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60489 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:M (auth: 1R), OB (auth: 2R)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:N (auth: 1S), PB (auth: 2S)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: 1T), QB (auth: 2T)
Chain Length:131
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60490 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:P (auth: 1U), RB (auth: 2U)
Chain Length:23
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60491 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:Q (auth: 1V), SB (auth: 2V)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60492 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:R (auth: 1W), TB (auth: 2W)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP3 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:S (auth: 1X), UB (auth: 2X)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:T (auth: 1Y), VB (auth: 2Y)
Chain Length:107
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:U (auth: 1Z), WB (auth: 2Z)
Chain Length:203
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Polymer Type:polyribonucleotide
Molecule:16s ribosomal RNA
Chain IDs:FA (auth: 1a), HC (auth: 2a)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:GA (auth: 1b), IC (auth: 2b)
Chain Length:120
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80371 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:HA (auth: 1c), JC (auth: 2c)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:IA (auth: 1d), KC (auth: 2d)
Chain Length:275
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:JA (auth: 1e), LC (auth: 2e)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:KA (auth: 1f), MC (auth: 2f)
Chain Length:203
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP8 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:LA (auth: 1g), NC (auth: 2g)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:MA (auth: 1h), OC (auth: 2h)
Chain Length:174
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY9 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:NA (auth: 1i), PC (auth: 2i)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80374 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:OA (auth: 1j), QC (auth: 2j)
Chain Length:97
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:PA (auth: 1k), RC (auth: 2k)
Chain Length:114
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:QA (auth: 1l), SC (auth: 2l)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:RA (auth: 1m), TC (auth: 2m)
Chain Length:116
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80377 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:SA (auth: 1n), UC (auth: 2n)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY6 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:TA (auth: 1o), VC (auth: 2o)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJ76 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:UA (auth: 1p), WC (auth: 2p)
Chain Length:149
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:VA (auth: 1q), XC (auth: 2q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:WA (auth: 1r), YC (auth: 2r)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:XA (auth: 1s), ZC (auth: 2s)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:YA (auth: 1t), AD (auth: 2t)
Chain Length:131
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:ZA (auth: 1u), BD (auth: 2u)
Chain Length:23
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:tRNA met
Chain IDs:AB (auth: 1x), CD (auth: 2x)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:Onc112
Chain IDs:BB (auth: 1y), DD (auth: 2y)
Chain Length:107
Number of Molecules:2
Biological Source:Oncopeltus fasciatus
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:ED (auth: A), FD (auth: B)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD QA ASP modified residue
2MA A A modified residue
2MG FA G modified residue
4OC FA C modified residue
4SU AB U 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
Ligand Molecules
ARG
K
MG
MPD
SF4
UNX
ZN
Primary Citation
The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex.
Nat.Struct.Mol.Biol. 22 470 475 (2015)
PMID: 25984971 DOI: 10.1038/nsmb.3034

Abstact

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.

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Primary Citation of related structures
4ZER