8ANA: Proline-rich antimicrobial peptide drosocin
Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit. Determined by electron microscopy at 2.1 Å resolution. Released 8 Mar 2023.
- Method
- Electron microscopy
- Resolution
- 2.1 Å
- Organisms
- Escherichia coli BW25113, Drosophila melanogaster
- Chains
- 32
- Atoms
- 86,461
- Mol. weight
- 1358.42 kDa
- Ligands
- ZN, A2G, SPM, MG
- Released
- 8 Mar 2023
Explore 8ANA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8ANA contains 125 α-helices and 203 β-strands across 30 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 0: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 1 |
| β-strand | 20-25 | 6 | 1 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 1 |
| β-strand | 45-53 | 9 | 1 |
Chain 1: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
Chain 2: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-11 | 4 | |
| β-strand | 15-16 | 2 | 5 |
| β-strand | 22-24 | 3 | 5 |
| α-helix | 25-26 | 2 | |
| α-helix | 38-44 | 7 | |
| β-strand | 48-49 | 2 | 5 |
| α-helix | 50-51 | 2 | |
| α-helix | 52-61 | 10 | |
Chain 3: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 8 |
| β-strand | 14-18 | 5 | 8 |
| β-strand | 23-27 | 5 | 8 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-37 | 3 | 8 |
Chain 4: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-16 | 7 | 9 |
| β-strand | 21-26 | 6 | 9 |
| β-strand | 33-34 | 2 | 9 |
| α-helix | 42-45 | 4 | |
| α-helix | 57-63 | 7 | |
Chain A: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-8 | 6 | |
| α-helix | 14-17 | 4 | |
Chain c: 10 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 13 |
| α-helix | 6-7 | 2 | |
| α-helix | 11-13 | 3 | |
| β-strand | 17-19 | 3 | 13 |
| β-strand | 24 | 1 | 14 |
| α-helix | 31-33 | 3 | |
| β-strand | 34-36 | 3 | 15 |
| β-strand | 43 | 1 | 16 |
| β-strand | 49 | 1 | 16 |
| β-strand | 54 | 1 | 17 |
| β-strand | 61-63 | 3 | 15 |
| β-strand | 65 | 1 | 14 |
| β-strand | 76-82 | 7 | 14 |
| β-strand | 91-96 | 6 | 14 |
| β-strand | 101-105 | 5 | 14 |
| β-strand | 107 | 1 | 18 |
| β-strand | 115-116 | 2 | 14 |
| β-strand | 129-131 | 3 | 19 |
| α-helix | 132-134 | 3 | |
| α-helix | 136 | 1 | |
| β-strand | 140-142 | 3 | 19 |
| β-strand | 144-145 | 2 | 20 |
| β-strand | 152-154 | 3 | 20 |
| β-strand | 162-168 | 7 | 19 |
| β-strand | 171-175 | 5 | 19 |
| β-strand | 181-185 | 5 | 19 |
| β-strand | 189-192 | 4 | 19 |
| β-strand | 195 | 1 | 18 |
| α-helix | 198-202 | 5 | |
| β-strand | 204 | 1 | 13 |
| α-helix | 208-213 | 6 | |
| β-strand | 216 | 1 | 17 |
| α-helix | 217-218 | 2 | |
| α-helix | 222-224 | 3 | |
| β-strand | 245 | 1 | 21 |
| β-strand | 251 | 1 | 21 |
| α-helix | 264-266 | 3 | |
| β-strand | 267-269 | 3 | 19 |
Chain d: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 22 |
| β-strand | 20-28 | 9 | 22 |
| β-strand | 32-38 | 7 | 23 |
| β-strand | 47-51 | 5 | 23 |
| α-helix | 62-71 | 10 | |
| β-strand | 80-83 | 4 | 23 |
| β-strand | 95-96 | 2 | 23 |
| α-helix | 98-101 | 4 | |
| β-strand | 106-112 | 7 | 22 |
| β-strand | 117-119 | 3 | 24 |
| α-helix | 121-124 | 4 | |
| α-helix | 127-129 | 3 | |
| α-helix | 155-156 | 2 | |
| β-strand | 163-165 | 3 | 24 |
| β-strand | 169-181 | 13 | 22 |
| β-strand | 186-190 | 5 | 22 |
| β-strand | 200-205 | 6 | 22 |
22 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 |
|---|
| 50S ribosomal protein L33 | 0 | protein | 55 | Escherichia coli BW25113 | P0A7N9 (AlphaFold model) |
| 50S ribosomal protein L34 | 1 | protein | 46 | Escherichia coli BW25113 | P0A7P5 (AlphaFold model) |
| 50S ribosomal protein L35 | 2 | protein | 65 | Escherichia coli BW25113 | P0A7Q1 (AlphaFold model) |
| 50S ribosomal protein L36 | 3 | protein | 38 | Escherichia coli BW25113 | P0A7Q6 (AlphaFold model) |
| 50S ribosomal protein L31 | 4 | protein | 70 | Escherichia coli BW25113 | P0A7M9 |
| Drosocin1 | A | protein | 19 | Drosophila melanogaster | P36193 |
| 23S ribosomal RNA | a | RNA | 2903 | Escherichia coli BW25113 | |
| 5S ribosomal RNA | b | RNA | 120 | Escherichia coli BW25113 | |
| 50S ribosomal protein L2 | c | protein | 273 | Escherichia coli BW25113 | P60422 |
| 50S ribosomal protein L3 | d | protein | 209 | Escherichia coli BW25113 | P60438 |
| 50S ribosomal protein L4 | e | protein | 201 | Escherichia coli BW25113 | P60723 |
| 50S ribosomal protein L5 | f | protein | 179 | Escherichia coli BW25113 | P62399 |
20 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>8ANA_1 50S ribosomal protein L33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK
Sequence of entity 2 (1), FASTA
>8ANA_2 50S ribosomal protein L34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK
Sequence of entity 3 (2), FASTA
>8ANA_3 50S ribosomal protein L35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA
Sequence of entity 4 (3), FASTA
>8ANA_4 50S ribosomal protein L36 (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG
Sequence of entity 5 (4), FASTA
>8ANA_5 50S ribosomal protein L31 (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK
Sequence of entity 6 (A), FASTA
>8ANA_6 Drosocin1 (chains A)
GKPRPYSPRPTSHPRPIRV
Sequence of entity 7 (a), FASTA
>8ANA_7 23S ribosomal RNA (chains a)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
GACCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCCUAAUCGGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU
Sequence of entity 8 (b), FASTA
>8ANA_8 5S ribosomal RNA (chains b)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 9 (c), FASTA
>8ANA_9 50S ribosomal protein L2 (chains c)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 10 (d), FASTA
>8ANA_10 50S ribosomal protein L3 (chains d)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 11 (e), FASTA
>8ANA_11 50S ribosomal protein L4 (chains e)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 12 (f), FASTA
>8ANA_12 50S ribosomal protein L5 (chains f)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| A2G | 2-acetamido-2-deoxy-alpha-D-galactopyranose | C8 H15 N O6 | 1 |
| SPM | Spermine | C10 H26 N4 | 1 |
| MG | Magnesium ion | Mg | 216 |
Primary citation
Structural basis for translation inhibition by the glycosylated drosocin peptide. Koller, T.O., Morici, M., Berger, M. et al. Nat Chem Biol (2023) 19:1072-1081. DOI 10.1038/s41589-023-01293-7 · PubMed
Other PDB entries of the same protein (UniProt P0A7N9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
- 9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
- 8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
- 8CGV 1.66 Å, Tiamulin bound to the 50S subunit
- 8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
- 8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
- 8CAM 1.86 Å, Evernimicin bound to the 50S subunit
- 9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
- 9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
- 9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
- 9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
- 9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
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