6OG7: 70S termination complex with RF2

Name: PDB 6OG7: 70S termination complex with RF2 bound to the UGA codon. Non-rotated ribosome with RF2 bound (Structure II)
Published: 2019-09-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

70S termination complex with RF2 bound to the UGA codon. Non-rotated ribosome with RF2 bound (Structure II). Determined by electron microscopy at 3.3 Å resolution. Released 25 Sept 2019.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Escherichia coli (strain K12), Escherichia coli, Escherichia coli K-12
Chains: 55
Atoms: 147,794
Mol. weight: 2204.91 kDa
Released: 25 Sept 2019

Explore 6OG7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OG7 contains 235 α-helices and 337 β-strands across 50 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 8: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	27-39	13
α-helix	46-48	3
α-helix	50-90	41
α-helix	93-117	25
β-strand	128-134	7	19
α-helix	139-158	20
β-strand	162-170	9	19
β-strand	176-184	9	19
β-strand	198-204	7	19
β-strand	213-223	11	19
β-strand	240-246	7	20
β-strand	258-265	8	20
β-strand	270-274	5	20
α-helix	280-313	34
β-strand	324-327	4	19
β-strand	332-335	4	19
β-strand	340-341	2	19
α-helix	345-348	4
α-helix	354	1
α-helix	355-360	6
α-helix	361-363	3

Chain a: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	21	1	103
α-helix	23-29	7
α-helix	30-32	3
β-strand	41-48	8	103
α-helix	55-57	3
β-strand	62-64	3	104
β-strand	160-162	3	104
β-strand	170-177	8	103
α-helix	182-197	16
β-strand	209-216	8	103
β-strand	219-224	6	103

Chain b: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	16-18	3	1
α-helix	30-32	3
β-strand	33-35	3	2
β-strand	42	1	3
β-strand	48	1	3
β-strand	53	1	4
β-strand	60-62	3	2
β-strand	64	1	5
β-strand	75-82	8	5
β-strand	89-95	7	5
β-strand	99-104	6	5
β-strand	106	1	6
β-strand	114-115	2	5
β-strand	117	1	7
β-strand	128-130	3	7
α-helix	135	1
β-strand	139-143	5	7
β-strand	153	1	7
β-strand	161-165	5	7
β-strand	170-175	6	7
β-strand	179-184	6	7
β-strand	188-191	4	7
β-strand	194	1	6
α-helix	199-201	3
β-strand	203	1	1
α-helix	207-211	5
β-strand	215	1	4
α-helix	221-223	3
β-strand	244	1	8
β-strand	250	1	8
α-helix	263-265	3
β-strand	266-268	3	7

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-15	7
α-helix	17-19	3
α-helix	20-22	3
β-strand	27-29	3	105
β-strand	36-38	3	105
β-strand	41	1	62
β-strand	47	1	106
β-strand	52	1	106

Chain c: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	10
β-strand	21-28	8	10
β-strand	32-38	7	11
β-strand	47-51	5	11
α-helix	62-71	10
β-strand	80-83	4	11
β-strand	95-96	2	11
α-helix	98-101	4
β-strand	106-112	7	10
α-helix	113-114	2
β-strand	118-119	2	12
α-helix	121-124	4
α-helix	127-131	5
β-strand	163-164	2	12
β-strand	169-179	11	10
β-strand	188-190	3	10
β-strand	200-205	6	10

Chain C: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	107
β-strand	19-25	7	107
α-helix	32-33	2
β-strand	34-37	4	107
β-strand	46-51	6	107

Chain d: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	14
β-strand	12-13	2	14
α-helix	16-19	4
α-helix	25-37	13
α-helix	68-69	2
α-helix	98-112	15
β-strand	118-121	4	15
α-helix	131-141	11
β-strand	148-150	3	15
α-helix	155-160	6
β-strand	169-171	3	15
α-helix	177-182	6
β-strand	186-189	4	15
α-helix	190-199	10

Chain D: 3 helices, 0 β-strands

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

42 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	b	protein	271	Escherichia coli (strain K12)	P60422 (AlphaFold model)
50S ribosomal protein L3	c	protein	209	Escherichia coli (strain K12)	P60438 (AlphaFold model)
50S ribosomal protein L4	d	protein	201	Escherichia coli (strain K12)	P60723 (AlphaFold model)
50S ribosomal protein L5	e	protein	177	Escherichia coli (strain K12)	P62399 (AlphaFold model)
50S ribosomal protein L6	f	protein	176	Escherichia coli (strain K12)	P0AG55
50S ribosomal protein L9	g	protein	149	Escherichia coli (strain K12)	P0A7R1
50S ribosomal protein L13	j	protein	142	Escherichia coli (strain K12)	P0AA10
50S ribosomal protein L14	k	protein	122	Escherichia coli (strain K12)	P0ADY3
50S ribosomal protein L15	l	protein	143	Escherichia coli (strain K12)	P02413
50S ribosomal protein L16	m	protein	136	Escherichia coli (strain K12)	P0ADY7
50S ribosomal protein L17	n	protein	120	Escherichia coli (strain K12)	P0AG44
50S ribosomal protein L18	o	protein	116	Escherichia coli (strain K12)	P0C018

43 more molecules are not listed.

Sequence of entity 1 (b), FASTA

>6OG7_1 50S ribosomal protein L2 (chains b)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS

Sequence of entity 2 (c), FASTA

>6OG7_2 50S ribosomal protein L3 (chains c)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 3 (d), FASTA

>6OG7_3 50S ribosomal protein L4 (chains d)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 4 (e), FASTA

>6OG7_4 50S ribosomal protein L5 (chains e)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR

Sequence of entity 5 (f), FASTA

>6OG7_5 50S ribosomal protein L6 (chains f)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 6 (g), FASTA

>6OG7_6 50S ribosomal protein L9 (chains g)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 7 (j), FASTA

>6OG7_7 50S ribosomal protein L13 (chains j)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 8 (k), FASTA

>6OG7_8 50S ribosomal protein L14 (chains k)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV

Sequence of entity 9 (l), FASTA

>6OG7_9 50S ribosomal protein L15 (chains l)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 10 (m), FASTA

>6OG7_10 50S ribosomal protein L16 (chains m)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Sequence of entity 11 (n), FASTA

>6OG7_11 50S ribosomal protein L17 (chains n)
MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV
ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE

Sequence of entity 12 (o), FASTA

>6OG7_12 50S ribosomal protein L18 (chains o)
DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQ
LKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF

Primary citation

Extensive ribosome and RF2 rearrangements during translation termination. Svidritskiy, E., Demo, G., Loveland, A.B. et al. Elife (2019) 8. DOI 10.7554/eLife.46850 · 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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