8ZTV: 70S ribosome arrested by PepNL with RF2

Name: PDB 8ZTV: 70S ribosome arrested by PepNL with RF2
Published: 2025-03-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

70S ribosome arrested by PepNL with RF2. Determined by electron microscopy at 2.9 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 57
Atoms: 143,031
Mol. weight: 2222.39 kDa
Ligands: MG, SPD, PUT, ZN
Released: 19 Mar 2025

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

Secondary structure: helices and β-sheets

8ZTV contains 244 α-helices and 314 β-strands across 51 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: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
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 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	16
β-strand	22-25	4	16
α-helix	38-44	7
β-strand	47-49	3	16
α-helix	52-61	10

Chain 3: 1 helix, 4 β-strands

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

Chain 4: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	28
β-strand	21-26	6	28
β-strand	32-34	3	28
α-helix	42-45	4

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	2
α-helix	25-27	3
β-strand	31-34	4	2
β-strand	38-41	4	2
α-helix	43-62	20
β-strand	67-70	4	3
α-helix	74-86	13
β-strand	90-92	3	3
α-helix	104-123	20
α-helix	125-128	4
α-helix	131-148	18
β-strand	160-163	4	3
α-helix	171-179	9
β-strand	183-187	5	3
β-strand	198-201	4	3
α-helix	207-226	20

Chain c: 8 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	6
α-helix	6-7	2
β-strand	17-19	3	6
β-strand	24	1	7
α-helix	31-33	3
β-strand	34	1	8
β-strand	37	1	9
β-strand	43	1	10
β-strand	49	1	10
β-strand	54	1	11
β-strand	60	1	9
β-strand	63	1	8
β-strand	65	1	7
β-strand	76-82	7	7
α-helix	90	1
β-strand	91-96	6	7
β-strand	101-105	5	7
β-strand	107	1	12
β-strand	115-116	2	7
β-strand	118	1	13
β-strand	129-131	3	13
α-helix	136	1
β-strand	140-142	3	13
β-strand	144-145	2	14
β-strand	152-154	3	14
β-strand	162-168	7	13
β-strand	171-175	5	13
β-strand	181-185	5	13
β-strand	189-192	4	13
β-strand	195	1	12
α-helix	198-202	5
β-strand	204	1	6
α-helix	208-213	6
β-strand	216	1	11
α-helix	217-218	2
α-helix	222-224	3
β-strand	245	1	15
β-strand	251	1	15
β-strand	267-269	3	13

Chain C: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	20-21	2	4
α-helix	26-46	21
α-helix	48-50	3
β-strand	52-58	7	4
β-strand	64-70	7	4
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-95	14
β-strand	99-105	7	4
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-155	8	5
α-helix	157-159	3
β-strand	164-171	8	5
β-strand	180-190	11	5
β-strand	195-206	12	5

43 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	1542	Escherichia coli
30S ribosomal protein S2	B	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	C	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	D	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	E	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6, fully modified isoform	F	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	G	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	H	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	I	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	J	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	K	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	L	protein	124	Escherichia coli	P0A7S3

45 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8ZTV_1 16S rRNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Sequence of entity 2 (B), FASTA

>8ZTV_2 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (C), FASTA

>8ZTV_3 30S ribosomal protein S3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (D), FASTA

>8ZTV_4 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (E), FASTA

>8ZTV_5 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (F), FASTA

>8ZTV_6 30S ribosomal protein S6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (G), FASTA

>8ZTV_7 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (H), FASTA

>8ZTV_8 30S ribosomal protein S8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (I), FASTA

>8ZTV_9 30S ribosomal protein S9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (J), FASTA

>8ZTV_10 30S ribosomal protein S10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (K), FASTA

>8ZTV_11 30S ribosomal protein S11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (L), FASTA

>8ZTV_12 30S ribosomal protein S12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	301
SPD	Spermidine	C7 H19 N3	7
PUT	1,4-diaminobutane	C4 H12 N2	1
ZN	Zinc ion	Zn	2

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

Primary citation

A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism. Ando, Y., Kobo, A., Niwa, T. et al. Nat Commun (2025) 16:2323-2323. DOI 10.1038/s41467-025-57659-z · 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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