7OJ0: 70S ribosome stalled with TnaC peptide and RF2

Name: PDB 7OJ0: Cryo-EM structure of 70S ribosome stalled with TnaC peptide and RF2
Published: 2021-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of 70S ribosome stalled with TnaC peptide and RF2. Determined by electron microscopy at 3.5 Å resolution. Released 15 Sept 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Escherichia coli K-12, Escherichia coli (strain K12)
Chains: 59
Atoms: 146,507
Mol. weight: 2211.43 kDa
Ligands: MG, TRP, ZN
Released: 15 Sept 2021

Explore 7OJ0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OJ0 contains 251 α-helices and 308 β-strands across 54 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: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	77
β-strand	20-25	6	77
β-strand	35-40	6	77
β-strand	45-52	8	77

Chain 1: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-15	7
α-helix	18-23	6
α-helix	25-37	13

Chain 2: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-13	6
β-strand	15-16	2	87
β-strand	22-24	3	87
α-helix	38-44	7
β-strand	48-49	2	87
α-helix	52-61	10

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	90
β-strand	14-19	6	90
β-strand	22-27	6	90
α-helix	31-33	3
β-strand	35-37	3	90

Chain 4: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	93
β-strand	20-26	7	93
β-strand	32-34	3	93
α-helix	42-45	4
α-helix	56-63	8

Chain 5: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	23-27	5	32
α-helix	34-47	14
α-helix	63-66	4
α-helix	67-69	3
α-helix	72-75	4
β-strand	83-87	5	32
α-helix	95-104	10

Chain 6: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	50
α-helix	15-20	6
α-helix	23-25	3
β-strand	28	1	18

Chain 7: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4

46 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
16S rRNA	A	RNA	1519	Escherichia coli K-12
30S ribosomal protein S2	B	protein	241	Escherichia coli (strain K12)	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	C	protein	233	Escherichia coli (strain K12)	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	D	protein	206	Escherichia coli (strain K12)	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	E	protein	167	Escherichia coli (strain K12)	P0A7W1 (AlphaFold model)
30S ribosomal protein S6, fully modified isoform	F	protein	135	Escherichia coli (strain K12)	P02358
30S ribosomal protein S7	G	protein	179	Escherichia coli (strain K12)	P02359
30S ribosomal protein S8	H	protein	130	Escherichia coli (strain K12)	P0A7W7
30S ribosomal protein S9	I	protein	130	Escherichia coli (strain K12)	P0A7X3
30S ribosomal protein S10	J	protein	103	Escherichia coli (strain K12)	P0A7R5
30S ribosomal protein S11	K	protein	129	Escherichia coli (strain K12)	P0A7R9
30S ribosomal protein S12	L	protein	124	Escherichia coli (strain K12)	P0A7S3

47 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7OJ0_1 16S rRNA (chains A)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUA
GUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAG
CCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGC
ACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUA
AAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCC
GCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCG
UUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAU
CCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGG
GUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAG
GCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUA
GAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCGGCGUGGCUU
CCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAA
UGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAA
GAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGA
ACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGU
CCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGA
GACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACG
ACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAA
GCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGU
CGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUAC
ACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGG
AGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGG
GGAACCUGCGGUUGGAUCA

Sequence of entity 2 (B), FASTA

>7OJ0_2 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (C), FASTA

>7OJ0_3 30S ribosomal protein S3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (D), FASTA

>7OJ0_4 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (E), FASTA

>7OJ0_5 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (F), FASTA

>7OJ0_6 30S ribosomal protein S6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (G), FASTA

>7OJ0_7 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (H), FASTA

>7OJ0_8 30S ribosomal protein S8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (I), FASTA

>7OJ0_9 30S ribosomal protein S9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (J), FASTA

>7OJ0_10 30S ribosomal protein S10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (K), FASTA

>7OJ0_11 30S ribosomal protein S11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (L), FASTA

>7OJ0_12 30S ribosomal protein S12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	308
TRP	Tryptophan	C11 H12 N2 O2	1
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide. Su, T., Kudva, R., Becker, T. et al. Nucleic Acids Res (2021) 49:9539-9547. DOI 10.1093/nar/gkab665 · 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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