5HD1: Antimicrobial peptide Pyrrhocoricin
Crystal structure of antimicrobial peptide Pyrrhocoricin bound to the Thermus thermophilus 70S ribosome. Determined by X-ray diffraction at 2.7 Å resolution. Released 6 Apr 2016.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organisms
- Thermus thermophilus HB8, Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Enterobacteria phage T4
- Chains
- 110
- Atoms
- 288,775
- Mol. weight
- 4470.89 kDa
- Ligands
- MG, ZN, SF4
- Released
- 6 Apr 2016
Explore 5HD1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5HD1 contains 506 α-helices and 653 β-strands across 100 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain 10: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 180 |
| β-strand | 30-31 | 2 | 181 |
| β-strand | 36-39 | 4 | 180 |
| β-strand | 45-47 | 3 | 181 |
| β-strand | 51-53 | 3 | 180 |
| β-strand | 59-61 | 3 | 180 |
| β-strand | 65-71 | 7 | 181 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-83 | 7 | 181 |
Chains 11 and 21: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-21 | 9 | 186 |
| α-helix | 25-27 | 3 | |
| β-strand | 33-42 | 10 | 186 |
| β-strand | 46-53 | 8 | 187 |
| β-strand | 56-63 | 8 | 187 |
| α-helix | 64-66 | 3 | |
| α-helix | 67-75 | 9 | |
| α-helix | 87-96 | 10 | |
Chain 12: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 18-40 | 23 | |
| α-helix | 48-69 | 22 | |
Chains 13 and 23: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 200 |
| α-helix | 17-26 | 10 | |
| β-strand | 34-38 | 5 | 200 |
| α-helix | 41-49 | 9 | |
| β-strand | 54-59 | 6 | 200 |
Chain 14: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| β-strand | 10-16 | 7 | 204 |
| β-strand | 21-26 | 6 | 204 |
| β-strand | 30-33 | 4 | 204 |
| α-helix | 37-39 | 3 | |
| α-helix | 59-61 | 3 | |
Chain 15: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 13-19 | 7 | |
| α-helix | 20-22 | 3 | |
| α-helix | 24-29 | 6 | |
| β-strand | 31-32 | 2 | 1 |
| β-strand | 39-40 | 2 | 1 |
| β-strand | 51-52 | 2 | 2 |
| β-strand | 55-56 | 2 | 2 |
Chain 16: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 5 |
| β-strand | 19-26 | 8 | 5 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 5 |
| β-strand | 45-52 | 8 | 5 |
Chain 17: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
81 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 23S Ribosomal RNA | 1A, 2A | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S Ribosomal RNA | 1B, 2B | RNA | 121 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L2 | 1D, 2D | protein | 276 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | 1E, 2E | protein | 206 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | 1F, 2F | protein | 210 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | 1G, 2G | protein | 182 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ0 (AlphaFold model) |
| 50S ribosomal protein L6 | 1H, 2H | protein | 180 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P0DOY8 |
| 50S ribosomal protein L9 | 1I, 2I | protein | 148 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SLQ1 |
| 50S ribosomal protein L13 | 1N, 2N | protein | 140 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60488 |
| 50S ribosomal protein L14 | 1O, 2O | protein | 122 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHP8 |
| 50S ribosomal protein L15 | 1P, 2P | protein | 150 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ7 |
| 50S ribosomal protein L16 | 1Q, 2Q | protein | 141 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60489 |
43 more molecules are not listed.
Sequence of entity 1 (1A, 2A), FASTA
>5HD1_1 23S Ribosomal RNA (chains 1A, 2A)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC
Sequence of entity 2 (1B, 2B), FASTA
>5HD1_2 5S Ribosomal RNA (chains 1B, 2B)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U
Sequence of entity 3 (1D, 2D), FASTA
>5HD1_3 50S ribosomal protein L2 (chains 1D, 2D)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 4 (1E, 2E), FASTA
>5HD1_4 50S ribosomal protein L3 (chains 1E, 2E)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 5 (1F, 2F), FASTA
>5HD1_5 50S ribosomal protein L4 (chains 1F, 2F)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 6 (1G, 2G), FASTA
>5HD1_6 50S ribosomal protein L5 (chains 1G, 2G)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 7 (1H, 2H), FASTA
>5HD1_7 50S ribosomal protein L6 (chains 1H, 2H)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 8 (1I, 2I), FASTA
>5HD1_8 50S ribosomal protein L9 (chains 1I, 2I)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 9 (1N, 2N), FASTA
>5HD1_9 50S ribosomal protein L13 (chains 1N, 2N)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 10 (1O, 2O), FASTA
>5HD1_10 50S ribosomal protein L14 (chains 1O, 2O)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Sequence of entity 11 (1P, 2P), FASTA
>5HD1_11 50S ribosomal protein L15 (chains 1P, 2P)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA
Sequence of entity 12 (1Q, 2Q), FASTA
>5HD1_12 50S ribosomal protein L16 (chains 1Q, 2Q)
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAARVAMVRHFRR
GGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRI
AGHKLPIKTKIVRRDAYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2601 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
Primary citation
Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Gagnon, M.G., Roy, R.N., Lomakin, I.B. et al. Nucleic Acids Res (2016) 44:2439-2450. DOI 10.1093/nar/gkw018 · PubMed
Other PDB entries of the same protein (UniProt P60405 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
- 8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
- 8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
- 6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
- 7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
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