9D89: E. coli 50S ribosomal subunit

Name: PDB 9D89: E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
Published: 2025-01-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement). Determined by electron microscopy at 1.95 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 1.95 Å
Organisms: Escherichia coli, Beatragus hunteri
Chains: 31
Atoms: 90,166
Mol. weight: 1280.9 kDa
Ligands: ZN, MG
Released: 22 Jan 2025

Explore 9D89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D89 contains 143 α-helices and 206 β-strands across 29 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
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 B: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	5
β-strand	22-24	3	5
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	5
α-helix	50-51	2
α-helix	52-61	10

Chain C: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	6
β-strand	15-19	5	6
β-strand	22-26	5	6
α-helix	31-33	3
β-strand	35-37	3	6

Chain f: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	8-12	5
α-helix	13-19	7
β-strand	31-38	8	34
α-helix	48-61	14
α-helix	64-65	2
β-strand	66-69	4	34
β-strand	74	1	35
β-strand	79	1	35
β-strand	84-91	8	34
α-helix	94-102	9
α-helix	103-107	5
α-helix	108-110	3
β-strand	122	1	34
β-strand	128-132	5	34
α-helix	135-137	3
β-strand	152-158	7	34
α-helix	163-172	10

Chain F: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
α-helix	6-7	2
β-strand	17-19	3	8
β-strand	24	1	9
α-helix	31-33	3
β-strand	34-36	3	10
β-strand	43	1	11
β-strand	49	1	11
β-strand	54	1	12
β-strand	61-63	3	10
β-strand	65	1	9
β-strand	76-82	7	9
β-strand	91-96	6	9
β-strand	101-105	5	9
β-strand	107	1	13
β-strand	115-116	2	9
β-strand	118	1	14
β-strand	129-131	3	14
α-helix	132-134	3
β-strand	140-142	3	14
β-strand	144	1	15
β-strand	154	1	15
β-strand	162-168	7	14
β-strand	171-175	5	14
β-strand	181-185	5	14
β-strand	189-192	4	14
β-strand	195	1	13
α-helix	198-202	5
β-strand	204	1	8
α-helix	208-213	6
β-strand	216	1	12
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	16
β-strand	251	1	16
α-helix	264-266	3
β-strand	267-269	3	14

Chain g: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8	1
β-strand	9-10	2	36
β-strand	16	1	37
β-strand	20	1	37
β-strand	23-27	5	37
β-strand	32-36	5	37
β-strand	41-44	4	38
β-strand	49-50	2	36
β-strand	51-54	4	38
α-helix	55	1
α-helix	61-80	20
β-strand	83-90	8	39
β-strand	95	1	40
β-strand	98	1	41
β-strand	102-105	4	41
β-strand	106	1	40
β-strand	113-116	4	41
β-strand	121-124	4	39
β-strand	130-135	6	39
α-helix	138-151	14
α-helix	153-155	3
β-strand	161-164	4	39
α-helix	173-176	4

Chain G: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	17
β-strand	21-28	8	17
α-helix	30-31	2
β-strand	32-38	7	18
β-strand	47-51	5	18
α-helix	57-59	3
α-helix	62-71	10
β-strand	80-83	4	18
α-helix	84-85	2
β-strand	95-96	2	18
α-helix	98-101	4
β-strand	106-112	7	17
α-helix	113-114	2
β-strand	115-119	5	19
α-helix	121-125	5
α-helix	127-129	3
β-strand	149	1	20
β-strand	152	1	20
α-helix	155-156	2
β-strand	163-166	4	19
β-strand	169-181	13	17
β-strand	186-190	5	17
β-strand	200-205	6	17

21 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	P0A7N9 (AlphaFold model)
50S ribosomal protein L34	1	protein	46	Escherichia coli	P0A7P5 (AlphaFold model)
50S ribosomal protein L35	B	protein	65	Escherichia coli	P0A7Q1 (AlphaFold model)
50S ribosomal protein L36	C	protein	38	Escherichia coli	P0A7Q6 (AlphaFold model)
23S rRNA	D	RNA	2728	Escherichia coli
5S rRNA	E	RNA	119	Escherichia coli
50S ribosomal protein L2	F	protein	273	Escherichia coli	P60422
50S ribosomal protein L3	G	protein	209	Escherichia coli	P60438
50S ribosomal protein L4	H	protein	201	Escherichia coli	P60723
50S ribosomal protein L15	I	protein	144	Escherichia coli	P02413
50S ribosomal protein L17	J	protein	118	Escherichia coli	P0AG44
Large ribosomal subunit protein uL23	K	protein	93	Escherichia coli	P0ADZ0

19 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9D89_1 50S ribosomal protein L33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>9D89_2 50S ribosomal protein L34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (B), FASTA

>9D89_3 50S ribosomal protein L35 (chains B)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (C), FASTA

>9D89_4 50S ribosomal protein L36 (chains C)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (D), FASTA

>9D89_5 23S rRNA (chains D)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACAGCUGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAG
GUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGG
UAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACU
GGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAG
GCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGA
AUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAAACCCGAUGCAAACUGCGAAUACCGG
AGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAA
CCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCC
CAGACAGCGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGC
UGCGGCAGCGACGCGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGUGAAGGUGUGCU
GUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGGGU
GAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGA
GUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGU
ACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCC
CGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGA
UGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGC
AUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAG
GCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAG
GCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAAUCAGUCGAAGAUACCA
GCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUAC
GGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGGCGCGAAGCUCUU
GAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAACGGUCCUAAGGUAGCGAAAUUCCU
UGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGA
GACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGAC
CCCGUGAACCUUUACUAUAGCUUGACACUGAACAUAUGUUCUAACGUUGGCCCGUGAUCC
GGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAAC
GGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUA
AGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCC
GGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGG
CUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUC
ACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGC
GAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAA
CUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGU
UGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUC
UAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCCUGAAGGAAC
GUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACC
GGUACUAAUGAACCGUGAGGCUUAACCU

Sequence of entity 6 (E), FASTA

>9D89_6 5S rRNA (chains E)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCA

Sequence of entity 7 (F), FASTA

>9D89_7 50S ribosomal protein L2 (chains F)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 8 (G), FASTA

>9D89_8 50S ribosomal protein L3 (chains G)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 9 (H), FASTA

>9D89_9 50S ribosomal protein L4 (chains H)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 10 (I), FASTA

>9D89_10 50S ribosomal protein L15 (chains I)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 11 (J), FASTA

>9D89_11 50S ribosomal protein L17 (chains J)
MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV
ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDR

Sequence of entity 12 (K), FASTA

>9D89_12 Large ribosomal subunit protein uL23 (chains K)
MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNT
LVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	204

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

Primary citation

Rumicidins are a family of mammalian host-defense peptides plugging the 70S ribosome exit tunnel. Panteleev, P.V., Pichkur, E.B., Kruglikov, R.N. et al. Nat Commun (2024) 15:8925-8925. DOI 10.1038/s41467-024-53309-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
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
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA

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