8P17: Small ribosomal subunit protein uS2

E167K RF2 on E. coli 70S release complex with UGG (Structure II). Determined by electron microscopy at 2.78 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 2.78 Å
Organisms: Escherichia coli, Escherichia coli K-12
Chains: 56
Atoms: 148,609
Mol. weight: 2253.31 kDa
Ligands: ZN, SPM, PUT, SPD
Released: 22 May 2024

Explore 8P17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P17 contains 266 α-helices and 317 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 6: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	27-42	16
α-helix	44-48	5
α-helix	50-90	41
α-helix	93-118	26
β-strand	128-134	7	15
α-helix	139-159	21
β-strand	162-170	9	15
β-strand	176-184	9	15
α-helix	188-192	5
α-helix	193-195	3
β-strand	197-204	8	15
β-strand	213-224	12	15
α-helix	227-229	3
α-helix	233-235	3
α-helix	236-238	3
β-strand	239-244	6	16
α-helix	245-246	2
α-helix	252-256	5
β-strand	260-265	6	16
β-strand	271-274	4	16
α-helix	280-313	34
α-helix	315-316	2
β-strand	324-327	4	15
β-strand	332-335	4	15
β-strand	341-342	2	15
α-helix	345-350	6
α-helix	354-363	10

Chain a: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	4
β-strand	21-26	6	4
α-helix	31	1
β-strand	32-34	3	4
α-helix	42-45	4
α-helix	56-63	8

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
β-strand	29-30	2	83
β-strand	37-38	2	83
β-strand	42	1	51
β-strand	48-49	2	84
β-strand	52-53	2	84

Chain B: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	87
α-helix	6-7	2
β-strand	17-19	3	87
β-strand	24	1	88
α-helix	31-33	3
β-strand	34-36	3	89
β-strand	43	1	90
β-strand	49	1	90
β-strand	54	1	91
β-strand	61-63	3	89
β-strand	65	1	88
β-strand	76-82	7	88
β-strand	91-96	6	88
β-strand	101-105	5	88
β-strand	107	1	92
β-strand	115-116	2	88
β-strand	118	1	93
β-strand	129-131	3	93
α-helix	136	1
β-strand	140-142	3	93
β-strand	144-145	2	94
β-strand	152-154	3	94
β-strand	162-168	7	93
β-strand	171-175	5	93
β-strand	181-185	5	93
β-strand	189-192	4	93
β-strand	195	1	92
α-helix	198-202	5
β-strand	204	1	87
α-helix	208-213	6
β-strand	216	1	91
α-helix	222-224	3
β-strand	245	1	95
β-strand	251	1	95
α-helix	264-266	3
β-strand	267-269	3	93

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	85
β-strand	20-25	6	85
α-helix	33-34	2
β-strand	35-40	6	85
β-strand	45-53	9	85

Chain C: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	1
β-strand	20-28	9	1
α-helix	31	1
β-strand	32-38	7	2
β-strand	47-51	5	2
α-helix	57-59	3
α-helix	62-71	10
β-strand	80-83	4	2
β-strand	95-96	2	2
α-helix	98-101	4
β-strand	106-112	7	1
α-helix	113-114	2
β-strand	115-119	5	3
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-166	4	3
β-strand	169-181	13	1
β-strand	186-190	5	1
β-strand	200-205	6	1

Chain d: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-23	6
α-helix	25-37	13

Chain D: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	7
β-strand	11-13	3	7
α-helix	16-19	4
α-helix	25-38	14
α-helix	68-69	2
α-helix	93-95	3
α-helix	98-115	18
β-strand	118-121	4	8
α-helix	131-140	10
β-strand	146-150	5	8
α-helix	155-161	7
β-strand	167-171	5	8
α-helix	172-174	3
α-helix	177-182	6
β-strand	185-189	5	8
α-helix	190-200	11

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 RNA	2	RNA	1542	Escherichia coli
Small ribosomal subunit protein uS2	g	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	h	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
Small ribosomal subunit protein uS4	i	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
Small ribosomal subunit protein uS5	j	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	k	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	l	protein	179	Escherichia coli	P02359
Small ribosomal subunit protein uS8	m	protein	130	Escherichia coli	P0A7W7
Small ribosomal subunit protein uS9	n	protein	130	Escherichia coli	P0A7X3
Small ribosomal subunit protein uS10	o	protein	103	Escherichia coli	P0A7R5
Small ribosomal subunit protein uS11	p	protein	129	Escherichia coli	P0A7R9
Small ribosomal subunit protein uS12	q	protein	124	Escherichia coli	P0A7S3

44 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>8P17_1 16S RNA (chains 2)
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 (g), FASTA

>8P17_2 Small ribosomal subunit protein uS2 (chains g)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (h), FASTA

>8P17_3 Small ribosomal subunit protein uS3 (chains h)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (i), FASTA

>8P17_4 Small ribosomal subunit protein uS4 (chains i)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (j), FASTA

>8P17_5 Small ribosomal subunit protein uS5 (chains j)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (k), FASTA

>8P17_6 30S ribosomal protein S6 (chains k)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (l), FASTA

>8P17_7 30S ribosomal protein S7 (chains l)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (m), FASTA

>8P17_8 Small ribosomal subunit protein uS8 (chains m)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (n), FASTA

>8P17_9 Small ribosomal subunit protein uS9 (chains n)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (o), FASTA

>8P17_10 Small ribosomal subunit protein uS10 (chains o)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (p), FASTA

>8P17_11 Small ribosomal subunit protein uS11 (chains p)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (q), FASTA

>8P17_12 Small ribosomal subunit protein uS12 (chains q)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
SPM	Spermine	C10 H26 N4	1
PUT	1,4-diaminobutane	C4 H12 N2	13
SPD	Spermidine	C7 H19 N3	13
MG	Magnesium ion	Mg	325

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

Primary citation

The compensatory mechanism of a naturally evolved E167K RF2 counteracting the loss of RF1 in bacteria. Pundir, S., Larsson, D.S.D., Selmer, M. et al. To be published.

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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