8CA7: Omadacycline and spectinomycin

Name: PDB 8CA7: Omadacycline and spectinomycin bound to the 30S ribosomal subunit head
Published: 2023-08-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Omadacycline and spectinomycin bound to the 30S ribosomal subunit head. Determined by electron microscopy at 2.06 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 2.06 Å
Organism: Escherichia coli BW25113
Chains: 9
Atoms: 18,093
Mol. weight: 626.74 kDa
Ligands: MG, SCM, U3B
Released: 2 Aug 2023

Explore 8CA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CA7 contains 42 α-helices and 36 β-strands across 8 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 C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	12	1	1
β-strand	16	1	1
α-helix	17-18	2
β-strand	20	1	2
α-helix	26-46	21
β-strand	52-58	7	2
β-strand	64-70	7	2
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-95	14
β-strand	99-105	7	2
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	3
α-helix	157-159	3
β-strand	164-171	8	3
β-strand	180-191	12	3
β-strand	194-206	13	3

Chain E: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	4
β-strand	28-33	6	4
β-strand	36	1	5
β-strand	50	1	5
β-strand	53	1	4
α-helix	56-64	9

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-69	12
α-helix	90-92	3
α-helix	93-110	18
α-helix	116-125	10

Chain I: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	6
β-strand	15-23	9	6
β-strand	28-30	3	6
β-strand	34	1	6
α-helix	35-38	4
α-helix	42-55	14
β-strand	61-68	8	6
α-helix	72-90	19
α-helix	95-100	6
α-helix	112-114	3
α-helix	124-127	4

Chain J: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	7
α-helix	15-32	18
β-strand	36-52	17	7
β-strand	62-76	15	7
β-strand	96-100	5	7

Chain M: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
β-strand	7-8	2	8
β-strand	14	1	9
α-helix	15-18	4
α-helix	19-21	3
α-helix	27-37	11
β-strand	44	1	9
α-helix	45-47	3
α-helix	50-62	13
α-helix	66-83	18
α-helix	86-93	8
α-helix	107-110	4

Chain N: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	21-32	12
α-helix	38-50	13
α-helix	53-55	3
α-helix	57-59	3
β-strand	73-74	2	10
β-strand	79-80	2	10
α-helix	81-89	9
β-strand	96-98	3	7

Chain S: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
α-helix	30	1
β-strand	31-33	3	11
β-strand	39	1	12
α-helix	42-44	3
β-strand	48-52	5	11
β-strand	57-61	5	11
β-strand	70	1	12
α-helix	71-74	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
16S rRNA	A	RNA	1540	Escherichia coli BW25113
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli BW25113	P0A7V3 (AlphaFold model)
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli BW25113	P0A7W1 (AlphaFold model)
30S ribosomal protein S7	G	protein	179	Escherichia coli BW25113	P02359 (AlphaFold model)
Small ribosomal subunit protein uS9	I	protein	130	Escherichia coli BW25113	P0A7X3 (AlphaFold model)
Small ribosomal subunit protein uS10	J	protein	103	Escherichia coli BW25113	P0A7R5
Small ribosomal subunit protein uS13	M	protein	118	Escherichia coli BW25113	P0A7S9
Small ribosomal subunit protein uS14	N	protein	101	Escherichia coli BW25113	P0AG59
Small ribosomal subunit protein uS19	S	protein	92	Escherichia coli BW25113	P0A7U3

Sequence of entity 1 (A), FASTA

>8CA7_1 16S rRNA (chains A)
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
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Sequence of entity 2 (C), FASTA

>8CA7_2 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 3 (E), FASTA

>8CA7_3 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 4 (G), FASTA

>8CA7_4 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 5 (I), FASTA

>8CA7_5 Small ribosomal subunit protein uS9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 6 (J), FASTA

>8CA7_6 Small ribosomal subunit protein uS10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 7 (M), FASTA

>8CA7_7 Small ribosomal subunit protein uS13 (chains M)
MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV
AKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK

Sequence of entity 8 (N), FASTA

>8CA7_8 Small ribosomal subunit protein uS14 (chains N)
MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQ
RNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW

Sequence of entity 9 (S), FASTA

>8CA7_9 Small ribosomal subunit protein uS19 (chains S)
MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPV
FVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	26
SCM	Spectinomycin	C14 H24 N2 O7	1
U3B	Omadacycline	C29 H40 N4 O7	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 P0A7V3 (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…
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8CF1 1.82 Å, Tetracycline bound to the 30S head
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
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
8CGI 1.89 Å, Pentacycline TP038 bound to the 30S head
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA
7K00 1.98 Å, Structure of the Bacterial Ribosome at 2 Angstrom Resolution

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