8E43: E. coli 50S ribosome

Name: PDB 8E43: E. coli 50S ribosome bound to compound streptogramin A analog 3336
Published: 2023-06-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E. coli 50S ribosome bound to compound streptogramin A analog 3336. Determined by electron microscopy at 2.09 Å resolution. Released 28 Jun 2023.

Method: Electron microscopy
Resolution: 2.09 Å
Organism: Escherichia coli
Chains: 10
Atoms: 74,031
Mol. weight: 1109.82 kDa
Ligands: UI0
Released: 28 Jun 2023

Explore 8E43 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E43 contains 50 α-helices and 70 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 K: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
α-helix	6-7	2
β-strand	17-19	3	1
β-strand	24	1	2
α-helix	31-33	3
β-strand	34-36	3	3
β-strand	43	1	4
β-strand	49	1	4
β-strand	54	1	5
β-strand	61-63	3	3
β-strand	65	1	2
β-strand	72	1	6
β-strand	76-82	7	2
β-strand	91-96	6	2
β-strand	101-105	5	2
β-strand	107	1	7
β-strand	115-116	2	2
β-strand	118	1	6
β-strand	129-131	3	6
α-helix	132-134	3
α-helix	136	1
β-strand	140-142	3	6
β-strand	144-145	2	8
β-strand	152-154	3	8
β-strand	162-166	5	6
β-strand	171-175	5	6
β-strand	181-185	5	6
β-strand	189-192	4	6
β-strand	195	1	7
α-helix	198-202	5
β-strand	204	1	1
α-helix	208-213	6
β-strand	216	1	5
α-helix	217-220	4
β-strand	267	1	6

Chain L: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
β-strand	51	1	9
β-strand	53	1	9
α-helix	57-60	4
α-helix	62-63	2
β-strand	74-76	3	10
α-helix	79-81	3
β-strand	89-90	2	11
α-helix	92-97	6
β-strand	107-109	3	10
β-strand	121-123	3	11
β-strand	126	1	10
α-helix	129-137	9
β-strand	141-143	3	11

Chain M: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	12
β-strand	11-13	3	12
α-helix	16-19	4
α-helix	25-38	14
α-helix	98-114	17
β-strand	118-121	4	13
α-helix	131-140	10
β-strand	146-150	5	13
α-helix	155-160	6
β-strand	167-171	5	13
α-helix	172-174	3
α-helix	177-182	6
β-strand	185-189	5	13
α-helix	190-200	11

Chain N: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	14
β-strand	21-28	8	14
α-helix	31	1
β-strand	32-38	7	15
β-strand	47-51	5	15
α-helix	57-59	3
α-helix	62-71	10
β-strand	80-83	4	15
β-strand	95-96	2	15
α-helix	98-101	4
β-strand	106-112	7	14
α-helix	113-114	2
β-strand	115-119	5	16
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-166	4	16
β-strand	169-181	13	14
β-strand	186-190	5	14
β-strand	200-205	6	14

Chain O: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	15-19	5	17
β-strand	24	1	18
α-helix	25-37	13
β-strand	53-57	5	17
α-helix	59-61	3
β-strand	63	1	18
α-helix	68-71	4
β-strand	73-76	4	19
β-strand	85-88	4	19
α-helix	89-95	7
α-helix	98-108	11
α-helix	110	1
α-helix	113-118	6
α-helix	119-121	3
β-strand	122-124	3	17
α-helix	133-135	3
α-helix	137	1
β-strand	138-139	2	17

Chain P: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	20
α-helix	14-24	11
β-strand	28	1	20
α-helix	29-37	9
α-helix	42-61	20
β-strand	70-78	9	20
α-helix	80-81	2
β-strand	82-87	6	21
α-helix	89-91	3
β-strand	93-98	6	21
β-strand	101-108	8	20

Chain Q: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	17-19	3
β-strand	29-30	2	22
β-strand	37-38	2	22

Chain R: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-21	4
α-helix	25-37	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
23S ribosomal RNA	I	RNA	2904	Escherichia coli
5S ribosomal RNA	J	RNA	118	Escherichia coli
50S ribosomal protein L2	K	protein	271	Escherichia coli	P60422 (AlphaFold model)
50S ribosomal protein L15	L	protein	144	Escherichia coli	P02413 (AlphaFold model)
50S ribosomal protein L4	M	protein	201	Escherichia coli	P60723 (AlphaFold model)
50S ribosomal protein L3	N	protein	209	Escherichia coli	P60438 (AlphaFold model)
50S ribosomal protein L13	O	protein	142	Escherichia coli	P0AA10
50S ribosomal protein L22	P	protein	110	Escherichia coli	P61175
50S ribosomal protein L32	Q	protein	56	Escherichia coli	P0A7N4
50S ribosomal protein L34	R	protein	46	Escherichia coli	P0A7P5

Sequence of entity 1 (I), FASTA

>8E43_1 23S ribosomal RNA (chains I)
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 2 (J), FASTA

>8E43_2 5S ribosomal RNA (chains J)
GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACG
CCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCA

Sequence of entity 3 (K), FASTA

>8E43_3 50S ribosomal protein L2 (chains K)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS

Sequence of entity 4 (L), FASTA

>8E43_4 50S ribosomal protein L15 (chains L)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 5 (M), FASTA

>8E43_5 50S ribosomal protein L4 (chains M)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 6 (N), FASTA

>8E43_6 50S ribosomal protein L3 (chains N)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 7 (O), FASTA

>8E43_7 50S ribosomal protein L13 (chains O)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 8 (P), FASTA

>8E43_8 50S ribosomal protein L22 (chains P)
METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEH
NDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR

Sequence of entity 9 (Q), FASTA

>8E43_9 50S ribosomal protein L32 (chains Q)
AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK

Sequence of entity 10 (R), FASTA

>8E43_10 50S ribosomal protein L34 (chains R)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Ligands and cofactors

ID	Name	Formula	Copies
UI0	(2R)-2-[(3S,4R,5E,10E,12E,14S,16R,23S,26aR)-16-fluoro-14-hydroxy-12-methyl-1,7,…	C40 H46 F N5 O8	1

Primary citation

Streptogramin A analogs. Li, Q., Pellegrino, J., Lee, D.J. et al. To be published.

Other PDB entries of the same protein (UniProt P60422 (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
8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142

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