8CF8: Eravacycline

Name: PDB 8CF8: Eravacycline bound to the 30S head
Published: 2023-08-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Eravacycline bound to the 30S head. Determined by electron microscopy at 2.2 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Escherichia coli BW25113
Chains: 9
Atoms: 19,324
Mol. weight: 635.7 kDa
Ligands: MG, YQM
Released: 2 Aug 2023

Explore 8CF8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CF8 contains 56 α-helices and 39 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 B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
β-strand	16-19	4	1
α-helix	20-22	3
α-helix	25-30	6
β-strand	33	1	1
β-strand	38-40	3	1
α-helix	43-61	19
β-strand	67-70	4	2
α-helix	77-80	4
β-strand	90-92	3	2
α-helix	104-123	20
α-helix	125-128	4
α-helix	131-148	18
β-strand	160-164	5	2
α-helix	170-179	10
β-strand	183-187	5	2
β-strand	200-201	2	2
α-helix	207-226	20

Chain C: 8 helices, 8 β-strands

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

Chain G: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	21-30	10
α-helix	36-54	19
α-helix	58-69	12
β-strand	73-79	7	5
β-strand	84-90	7	5
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-128	13
α-helix	133-147	15
α-helix	149-151	3

Chain I: 7 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	33-34	2	6
α-helix	35-38	4
α-helix	42-55	14
β-strand	61-68	8	6
α-helix	72-90	19
α-helix	92-94	3
α-helix	95-100	6
α-helix	111-114	4
α-helix	124-127	4

Chain J: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	7
α-helix	15-31	17
β-strand	35-52	18	7
β-strand	62-77	16	7
α-helix	81-88	8
α-helix	92-93	2
β-strand	96-101	6	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	50-60	11
α-helix	66-83	18
α-helix	86-93	8
α-helix	107-110	4

Chain N: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-32	29
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: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	13-25	13
β-strand	31-33	3	11
β-strand	39	1	12
α-helix	40-41	2
α-helix	42-44	3
β-strand	48-52	5	11
β-strand	57-61	5	11
α-helix	64-66	3
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
30S ribosomal protein S2	B	protein	241	Escherichia coli BW25113	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli BW25113	P0A7V3 (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

>8CF8_1 16S rRNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGCCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Sequence of entity 2 (B), FASTA

>8CF8_2 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (C), FASTA

>8CF8_3 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (G), FASTA

>8CF8_4 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 5 (I), FASTA

>8CF8_5 Small ribosomal subunit protein uS9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 6 (J), FASTA

>8CF8_6 Small ribosomal subunit protein uS10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 7 (M), FASTA

>8CF8_7 Small ribosomal subunit protein uS13 (chains M)
MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV
AKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK

Sequence of entity 8 (N), FASTA

>8CF8_8 Small ribosomal subunit protein uS14 (chains N)
MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQ
RNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW

Sequence of entity 9 (S), FASTA

>8CF8_9 Small ribosomal subunit protein uS19 (chains S)
MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPV
FVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	32
YQM	Eravacycline	C27 H31 F N4 O8	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 P0A7V0 (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…
4ODN 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide
7OXH 1.7 Å, ttSlyD with pseudo-wild-type S2 peptide
4ODP 1.75 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
4ODM 1.75 Å, Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8CF1 1.82 Å, Tetracycline bound to the 30S head
7OXJ 1.85 Å, ttSlyD with M8A pseudo-wild-type S2 peptide
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

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