8B0X: Translating 70S ribosome in the unrotated state

Name: PDB 8B0X: Translating 70S ribosome in the unrotated state (P and E, tRNAs)
Published: 2022-11-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Translating 70S ribosome in the unrotated state (P and E, tRNAs). Determined by electron microscopy at 1.55 Å resolution. Released 30 Nov 2022.

Method: Electron microscopy
Resolution: 1.55 Å
Organism: Escherichia coli B
Chains: 53
Atoms: 151,507
Mol. weight: 2185.23 kDa
Ligands: ZN, MG
Released: 30 Nov 2022

Explore 8B0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B0X contains 264 α-helices and 304 β-strands across 48 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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	14-16	3	4
β-strand	22-24	3	4
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	4
α-helix	50-51	2
α-helix	52-61	10

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	5
β-strand	14-19	6	5
β-strand	22-27	6	5
α-helix	31-33	3
β-strand	35-37	3	5

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	19
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-34	4	19
β-strand	38-41	4	19
α-helix	43-62	20
β-strand	67-70	4	20
α-helix	77-85	9
β-strand	90-92	3	20
α-helix	95-97	3
α-helix	104-123	20
α-helix	125-127	3
α-helix	132-148	17
β-strand	160-164	5	20
α-helix	170-179	10
β-strand	183-187	5	20
α-helix	193-195	3
β-strand	198-201	4	20
α-helix	207-226	20

Chain c: 9 helices, 29 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	34-35	2	8
β-strand	43	1	9
β-strand	49	1	9
β-strand	54	1	10
α-helix	61	1
β-strand	62-63	2	8
β-strand	65	1	7
β-strand	76-82	7	7
β-strand	91-96	6	7
β-strand	101-105	5	7
β-strand	107	1	11
β-strand	115-116	2	7
β-strand	118	1	12
β-strand	129-131	3	12
α-helix	132-134	3
β-strand	140-142	3	12
β-strand	144-145	2	13
β-strand	152-154	3	13
β-strand	162-168	7	12
β-strand	171-175	5	12
β-strand	181-185	5	12
β-strand	189-192	4	12
β-strand	195	1	11
α-helix	198-202	5
β-strand	204	1	6
α-helix	208-212	5
β-strand	216	1	10
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	14
β-strand	251	1	14
α-helix	264-266	3
β-strand	267-269	3	12

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20-21	2	23
α-helix	26-46	21
β-strand	52-58	7	23
β-strand	64-70	7	23
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-95	14
β-strand	99-105	7	23
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	24
α-helix	157-159	3
β-strand	164-171	8	24
β-strand	180-191	12	24
β-strand	194-206	13	24

Chain d: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	15
β-strand	21-28	8	15
α-helix	30-31	2
β-strand	32-38	7	16
α-helix	40-43	4
β-strand	47-51	5	16
α-helix	57-59	3
α-helix	62-71	10
β-strand	79-83	5	16
β-strand	95-96	2	16
α-helix	98-101	4
β-strand	106-112	7	15
α-helix	113-114	2
β-strand	115-119	5	17
α-helix	121-125	5
α-helix	127-129	3
β-strand	149	1	18
β-strand	152	1	18
α-helix	155-156	2
β-strand	163-166	4	17
β-strand	169-181	13	15
β-strand	186-190	5	15
β-strand	200-205	6	15

40 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 B	P0A7N9 (AlphaFold model)
50S ribosomal protein L34	1	protein	46	Escherichia coli B	P0A7P5 (AlphaFold model)
50S ribosomal protein L35	2	protein	65	Escherichia coli B	P0A7Q1 (AlphaFold model)
50S ribosomal protein L36	3	protein	38	Escherichia coli B	P0A7Q6 (AlphaFold model)
16S rRNA	A	RNA	1554	Escherichia coli B
30S ribosomal protein S2	B	protein	241	Escherichia coli B	P0A7V0
30S ribosomal protein S3	C	protein	233	Escherichia coli B	P0A7V3
30S ribosomal protein S4	D	protein	206	Escherichia coli B	P0A7V8
30S ribosomal protein S5	E	protein	167	Escherichia coli B	P0A7W1
30S ribosomal protein S6	F	protein	135	Escherichia coli B	P02358
30S ribosomal protein S7	G	protein	179	Escherichia coli B	P02359
30S ribosomal protein S8	H	protein	130	Escherichia coli B	P0A7W7

41 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8B0X_1 50S ribosomal protein L33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8B0X_2 50S ribosomal protein L34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8B0X_3 50S ribosomal protein L35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8B0X_4 50S ribosomal protein L36 (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (A), FASTA

>8B0X_5 16S rRNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGCAGCUUGCUGCUUCGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUAGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUACCUUAAAGAAGC

Sequence of entity 6 (B), FASTA

>8B0X_6 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 7 (C), FASTA

>8B0X_7 30S ribosomal protein S3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 8 (D), FASTA

>8B0X_8 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 9 (E), FASTA

>8B0X_9 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 10 (F), FASTA

>8B0X_10 30S ribosomal protein S6 (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 11 (G), FASTA

>8B0X_11 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 12 (H), FASTA

>8B0X_12 30S ribosomal protein S8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	361

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

Primary citation

The translating bacterial ribosome at 1.55 angstrom resolution generated by cryo-EM imaging services. Fromm, S.A., O'Connor, K.M., Purdy, M. et al. Nat Commun (2023) 14:1095-1095. DOI 10.1038/s41467-023-36742-3 · PubMed

Other PDB entries of the same protein (UniProt P0A7N9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA

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