8AKN: Proline-rich antimicrobial peptide drosocin

Name: PDB 8AKN: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome
Published: 2023-03-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome. Determined by electron microscopy at 2.3 Å resolution. Released 8 Mar 2023.

Method: Electron microscopy
Resolution: 2.3 Å
Organisms: Escherichia coli BW25113, Drosophila melanogaster
Chains: 57
Atoms: 146,513
Mol. weight: 2240.07 kDa
Ligands: ZN, A2G, MG, SPM
Released: 8 Mar 2023

Explore 8AKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AKN contains 260 α-helices and 319 β-strands across 51 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	45-52	8	1

Chain 1: 3 helices, 0 β-strands

Element	Residues	Length
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	14-16	3	8
β-strand	22-24	3	8
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	8
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	9
β-strand	14-19	6	9
β-strand	22-27	6	9
α-helix	31-33	3
β-strand	35-37	3	9

Chain 4: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	11
β-strand	21-26	6	11
β-strand	32-34	3	11
α-helix	42-45	4
α-helix	56-63	8

Chain A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	14-16	3

Chain c: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	16
β-strand	17-19	3	16
α-helix	31-33	3
β-strand	34-36	3	17
β-strand	43	1	18
β-strand	49	1	18
β-strand	54	1	19
β-strand	61-63	3	17
β-strand	65	1	20
β-strand	76-82	7	20
β-strand	91-96	6	20
β-strand	101-105	5	20
β-strand	107	1	21
β-strand	115-116	2	20
β-strand	118	1	22
β-strand	129-131	3	22
α-helix	136	1
β-strand	140-142	3	22
β-strand	144	1	23
β-strand	154	1	23
β-strand	162-168	7	22
β-strand	171-175	5	22
β-strand	181-185	5	22
β-strand	189-192	4	22
β-strand	195	1	21
α-helix	198-202	5
β-strand	204	1	16
α-helix	208-213	6
β-strand	216	1	19
α-helix	222-224	3
β-strand	245	1	24
β-strand	251	1	24
α-helix	264-266	3
β-strand	267-269	3	22

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-19	4	14
α-helix	25-30	6
β-strand	31-34	4	14
β-strand	38-41	4	14
α-helix	43-62	20
β-strand	67-70	4	15
α-helix	77-86	10
β-strand	90-92	3	15
α-helix	104-123	20
α-helix	131-148	18
β-strand	160-164	5	15
α-helix	170-179	10
β-strand	183-187	5	15
β-strand	198-201	4	15
α-helix	207-225	19

43 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
16S ribosomal RNA	B	RNA	1534	Escherichia coli BW25113
30S ribosomal protein S2	C	protein	241	Escherichia coli BW25113	P0A7V0
30S ribosomal protein S3	D	protein	233	Escherichia coli BW25113	P0A7V3
30S ribosomal protein S4	E	protein	206	Escherichia coli BW25113	P0A7V8
30S ribosomal protein S5	F	protein	167	Escherichia coli BW25113	P0A7W1
30S ribosomal protein S6, fully modified isoform	G	protein	135	Escherichia coli BW25113	P02358

45 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8AKN_1 50S ribosomal protein L33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8AKN_2 50S ribosomal protein L34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8AKN_3 50S ribosomal protein L35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8AKN_4 50S ribosomal protein L36 (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (4), FASTA

>8AKN_5 50S ribosomal protein L31 (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK

Sequence of entity 6 (A), FASTA

>8AKN_6 Drosocin1 (chains A)
GKPRPYSPRPTSHPRPIRV

Sequence of entity 7 (B), FASTA

>8AKN_7 16S ribosomal RNA (chains B)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA

Sequence of entity 8 (C), FASTA

>8AKN_8 30S ribosomal protein S2 (chains C)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 9 (D), FASTA

>8AKN_9 30S ribosomal protein S3 (chains D)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 10 (E), FASTA

>8AKN_10 30S ribosomal protein S4 (chains E)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 11 (F), FASTA

>8AKN_11 30S ribosomal protein S5 (chains F)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 12 (G), FASTA

>8AKN_12 30S ribosomal protein S6, fully modified isoform (chains G)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

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
MG	Magnesium ion	Mg	305
SPM	Spermine	C10 H26 N4	1

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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