7TOS: E. coli 70S ribosomes

Name: PDB 7TOS: E. coli 70S ribosomes bound with the ALS/FTD-associated dipeptide repeat protein PR20
Published: 2022-05-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E. coli 70S ribosomes bound with the ALS/FTD-associated dipeptide repeat protein PR20. Determined by electron microscopy at 2.9 Å resolution. Released 25 May 2022.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 56
Atoms: 145,427
Mol. weight: 2170.37 kDa
Released: 25 May 2022

Explore 7TOS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TOS contains 246 α-helices and 336 β-strands across 53 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 L02: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	5-6	2
β-strand	16-18	3	1
β-strand	23	1	2
α-helix	30-32	3
β-strand	33-34	2	3
β-strand	42	1	4
β-strand	48	1	4
β-strand	53	1	5
β-strand	61-62	2	3
β-strand	64	1	2
β-strand	71	1	6
β-strand	75-81	7	2
β-strand	90-95	6	2
β-strand	100-104	5	2
β-strand	106	1	7
β-strand	114-115	2	2
β-strand	117	1	6
β-strand	128-130	3	8
α-helix	135	1
β-strand	139-141	3	8
β-strand	143	1	9
β-strand	153	1	9
β-strand	161-167	7	8
β-strand	170-174	5	8
β-strand	180-184	5	8
β-strand	188-191	4	8
β-strand	194	1	7
α-helix	199-201	3
β-strand	203	1	1
α-helix	207-211	5
β-strand	215	1	5
α-helix	216-217	2
β-strand	244	1	10
β-strand	250	1	10
α-helix	263-265	3
β-strand	266-268	3	8

Chain L03: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	13
β-strand	21-28	8	13
β-strand	32-38	7	14
β-strand	47-52	6	14
α-helix	62-71	10
β-strand	77-83	7	14
β-strand	95-96	2	14
α-helix	98-101	4
β-strand	106-112	7	13
α-helix	113-115	3
β-strand	117-119	3	15
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-165	3	15
β-strand	169-179	11	13
β-strand	188-190	3	13
β-strand	200-205	6	13

Chain L04: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	18
β-strand	12-13	2	18
α-helix	16-20	5
α-helix	25-38	14
α-helix	68-69	2
α-helix	98-114	17
β-strand	118-120	3	19
α-helix	131-140	10
β-strand	146-150	5	19
α-helix	155-160	6
β-strand	169-171	3	19
α-helix	179-182	4
β-strand	185-188	4	19
α-helix	190-200	11

Chain L05: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	7-11	5
α-helix	12-16	5
α-helix	24-26	3
β-strand	30-37	8	20
α-helix	41-43	3
α-helix	47-59	13
α-helix	63-64	2
β-strand	65-68	4	20
β-strand	83-90	8	20
α-helix	94-103	10
β-strand	121	1	20
β-strand	127-131	5	20
β-strand	151-157	7	20
α-helix	162-170	9

Chain L06: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8-9	2	22
α-helix	10	1
β-strand	15-19	5	23
β-strand	22-26	5	23
β-strand	31-35	5	23
β-strand	40-43	4	24
β-strand	48-49	2	22
β-strand	50-53	4	24
α-helix	54	1
α-helix	60-79	20
β-strand	82-89	8	25
β-strand	94-98	5	26
β-strand	101-105	5	26
β-strand	112-115	4	26
α-helix	116	1
β-strand	121-126	6	25
β-strand	129-134	6	25
α-helix	137-150	14
α-helix	152-154	3
β-strand	160-163	4	25

Chain L09: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	28
α-helix	23-25	3
α-helix	26-30	5
α-helix	31-33	3
β-strand	36-37	2	28
α-helix	41-46	6
α-helix	47-51	5
α-helix	63-70	8
β-strand	78-82	5	29
β-strand	85	1	30
β-strand	88	1	30
α-helix	96-104	9
β-strand	115-116	2	29
β-strand	127-133	7	29
β-strand	139-148	10	29

Chain L1: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	21	1	109
α-helix	23-29	7
β-strand	41-47	7	109
α-helix	55-57	3
β-strand	60-63	4	110
β-strand	161-164	4	110
β-strand	170-177	8	109
α-helix	182-197	16
β-strand	212-215	4	109
β-strand	222-224	3	109

Chain L10: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
β-strand	24-27	4	33
α-helix	34-36	3
α-helix	37-41	5
α-helix	42-47	6
α-helix	72-74	3
β-strand	83-86	4	33
α-helix	95-100	6
α-helix	111-113	3

45 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 L2	L02	protein	271	Escherichia coli	P60422 (AlphaFold model)
50S ribosomal protein L3	L03	protein	209	Escherichia coli	P60438 (AlphaFold model)
50S ribosomal protein L4	L04	protein	201	Escherichia coli	P60723 (AlphaFold model)
50S ribosomal protein L5	L05	protein	177	Escherichia coli	P62399 (AlphaFold model)
50S ribosomal protein L6	L06	protein	176	Escherichia coli	P0AG55
50S ribosomal protein L9	L09	protein	149	Escherichia coli	P0A7R1
50S ribosomal protein L10	L10	protein	131	Escherichia coli	P0A7J3
50S ribosomal protein L11	L11	protein	141	Escherichia coli	P0A7J7
50S ribosomal protein L13	L13	protein	142	Escherichia coli	P0AA10
50S ribosomal protein L14	L14	protein	122	Escherichia coli	P0ADY3
50S ribosomal protein L15	L15	protein	143	Escherichia coli	P02413
50S ribosomal protein L16	L16	protein	136	Escherichia coli	P0ADY7

44 more molecules are not listed.

Sequence of entity 1 (L02), FASTA

>7TOS_1 50S ribosomal protein L2 (chains L02)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS

Sequence of entity 2 (L03), FASTA

>7TOS_2 50S ribosomal protein L3 (chains L03)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 3 (L04), FASTA

>7TOS_3 50S ribosomal protein L4 (chains L04)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 4 (L05), FASTA

>7TOS_4 50S ribosomal protein L5 (chains L05)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR

Sequence of entity 5 (L06), FASTA

>7TOS_5 50S ribosomal protein L6 (chains L06)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 6 (L09), FASTA

>7TOS_6 50S ribosomal protein L9 (chains L09)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 7 (L10), FASTA

>7TOS_7 50S ribosomal protein L10 (chains L10)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPT

Sequence of entity 8 (L11), FASTA

>7TOS_8 50S ribosomal protein L11 (chains L11)
AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITV
YADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGAD
IEAMTRSIEGTARSMGLVVED

Sequence of entity 9 (L13), FASTA

>7TOS_9 50S ribosomal protein L13 (chains L13)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 10 (L14), FASTA

>7TOS_10 50S ribosomal protein L14 (chains L14)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV

Sequence of entity 11 (L15), FASTA

>7TOS_11 50S ribosomal protein L15 (chains L15)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 12 (L16), FASTA

>7TOS_12 50S ribosomal protein L16 (chains L16)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Primary citation

Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM. Loveland, A.B., Svidritskiy, E., Susorov, D. et al. Nat Commun (2022) 13:2776-2776. DOI 10.1038/s41467-022-30418-0 · PubMed

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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