8CEU: Retapamulin and Capreomycin

Name: PDB 8CEU: Retapamulin and Capreomycin bound to the 50S subunit
Published: 2023-07-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Retapamulin and Capreomycin bound to the 50S subunit. Determined by electron microscopy at 1.83 Å resolution. Released 26 Jul 2023.

Method: Electron microscopy
Resolution: 1.83 Å
Organisms: Escherichia coli BW25113, Streptomyces californicus
Chains: 38
Atoms: 92,830
Mol. weight: 1357.5 kDa
Ligands: MG, G34, ZN
Released: 26 Jul 2023

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

Secondary structure: helices and β-sheets

8CEU contains 135 α-helices and 195 β-strands across 28 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
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	4
β-strand	22-24	3	4
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	4
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	6
β-strand	14-19	6	6
β-strand	22-27	6	6
α-helix	31-33	3
β-strand	35-37	3	6

Chain c: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
α-helix	6-7	2
β-strand	17-19	3	9
β-strand	24	1	10
α-helix	31-33	3
β-strand	34-36	3	11
β-strand	43	1	12
β-strand	49	1	12
β-strand	54	1	13
β-strand	61-63	3	11
β-strand	65	1	10
β-strand	76-82	7	10
β-strand	91-96	6	10
β-strand	101-105	5	10
β-strand	107	1	14
β-strand	115-116	2	10
β-strand	118	1	15
β-strand	129-131	3	15
α-helix	136	1
β-strand	140-142	3	15
β-strand	144-145	2	16
β-strand	152-154	3	16
β-strand	162-168	7	15
β-strand	171-175	5	15
β-strand	181-185	5	15
β-strand	189-192	4	15
β-strand	195	1	14
α-helix	198-202	5
β-strand	204	1	9
α-helix	208-213	6
β-strand	216	1	13
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	17
β-strand	251	1	17
α-helix	264-266	3
β-strand	267-269	3	15

Chain d: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	18
β-strand	21-28	8	18
β-strand	32-38	7	19
β-strand	47-51	5	19
α-helix	57-59	3
α-helix	62-71	10
β-strand	80-83	4	19
α-helix	84-85	2
β-strand	95-96	2	19
α-helix	98-101	4
β-strand	106-112	7	18
α-helix	113-115	3
β-strand	117-119	3	20
α-helix	121-125	5
α-helix	127-129	3
β-strand	149	1	21
β-strand	152	1	21
α-helix	155-156	2
β-strand	163-165	3	20
β-strand	169-181	13	18
β-strand	186-190	5	18
β-strand	200-205	6	18

Chain e: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
α-helix	25-38	14
α-helix	68-69	2
α-helix	98-114	17
β-strand	118-121	4	22
α-helix	131-140	10
β-strand	146-150	5	22
α-helix	155-161	7
β-strand	167-171	5	22
α-helix	172-174	3
α-helix	177-182	6
β-strand	185-189	5	22
α-helix	190-200	11

Chain f: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-12	5
α-helix	13-19	7
α-helix	25-27	3
β-strand	31-37	7	23
α-helix	58-61	4
α-helix	64-65	2
β-strand	66	1	23
β-strand	74	1	24
β-strand	79	1	24
β-strand	88-91	4	23
α-helix	94-101	8
β-strand	128-131	4	23
β-strand	153-158	6	23
α-helix	163-172	10

20 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
Large ribosomal subunit protein bL33	0	protein	55	Escherichia coli BW25113	P0A7N9 (AlphaFold model)
Large ribosomal subunit protein bL34	1	protein	46	Escherichia coli BW25113	P0A7P5 (AlphaFold model)
Large ribosomal subunit protein bL35	2	protein	65	Escherichia coli BW25113	P0A7Q1 (AlphaFold model)
Large ribosomal subunit protein bL36A	3	protein	38	Escherichia coli BW25113	P0A7Q6 (AlphaFold model)
23S rRNA	a	RNA	2904	Escherichia coli BW25113
5S rRNA	b	RNA	120	Escherichia coli BW25113
Large ribosomal subunit protein uL2	c	protein	273	Escherichia coli BW25113	P60422
Large ribosomal subunit protein uL3	d	protein	209	Escherichia coli BW25113	P60438
Large ribosomal subunit protein uL4	e	protein	201	Escherichia coli BW25113	P60723
Large ribosomal subunit protein uL5	f	protein	179	Escherichia coli BW25113	P62399
Large ribosomal subunit protein uL6	g	protein	177	Escherichia coli BW25113	P0AG55
Large ribosomal subunit protein bL9	h	protein	149	Escherichia coli BW25113	P0A7R1

19 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8CEU_1 Large ribosomal subunit protein bL33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8CEU_2 Large ribosomal subunit protein bL34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8CEU_3 Large ribosomal subunit protein bL35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8CEU_4 Large ribosomal subunit protein bL36A (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (a), FASTA

>8CEU_5 23S rRNA (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
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU

Sequence of entity 6 (b), FASTA

>8CEU_6 5S rRNA (chains b)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 7 (c), FASTA

>8CEU_7 Large ribosomal subunit protein uL2 (chains c)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 8 (d), FASTA

>8CEU_8 Large ribosomal subunit protein uL3 (chains d)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 9 (e), FASTA

>8CEU_9 Large ribosomal subunit protein uL4 (chains e)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 10 (f), FASTA

>8CEU_10 Large ribosomal subunit protein uL5 (chains f)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 11 (g), FASTA

>8CEU_11 Large ribosomal subunit protein uL6 (chains g)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 12 (h), FASTA

>8CEU_12 Large ribosomal subunit protein bL9 (chains h)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	220
G34	Retapamulin	C30 H47 N O4 S	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (K) are not listed.

Primary citation

Structural conservation of antibiotic interaction with ribosomes. Paternoga, H., Crowe-McAuliffe, C., Bock, L.V. et al. Nat Struct Mol Biol (2023) 30:1380-1392. DOI 10.1038/s41594-023-01047-y · 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
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)
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA

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