6H4N: 30S ribosomal protein S2

Name: PDB 6H4N: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome
Published: 2018-09-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome. Determined by electron microscopy at 3.0 Å resolution. Released 5 Sept 2018.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Escherichia coli BW25113
Chains: 57
Atoms: 147,282
Mol. weight: 2216.4 kDa
Released: 5 Sept 2018

Explore 6H4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H4N contains 228 α-helices and 353 β-strands across 52 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-15	7
β-strand	28-29	2	96
β-strand	36-37	2	96
β-strand	41	1	59
β-strand	47	1	97
β-strand	52	1	97

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	98
β-strand	19-23	5	98
β-strand	34-39	6	98
β-strand	44-51	8	98

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-37	13

Chain 3: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	7-12	6
β-strand	14-15	2	108
β-strand	21-23	3	108
α-helix	37-41	5
β-strand	47-48	2	108
α-helix	49-50	2
α-helix	55-60	6

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	112
β-strand	14-19	6	112
β-strand	22-27	6	112
α-helix	31-33	3
β-strand	35-36	2	112

Chain 6: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	115
β-strand	22-26	5	115
β-strand	32-33	2	115
α-helix	57-60	4

Chain b: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	32	1	2
β-strand	38	1	2
α-helix	42-60	19
β-strand	66-69	4	3
α-helix	76-84	9
β-strand	89-91	3	3
α-helix	103-121	19
α-helix	130-147	18
β-strand	159-162	4	3
α-helix	169-177	9
β-strand	182-184	3	3
β-strand	185-186	2	4
β-strand	199-200	2	4
α-helix	206-223	18

Chain c: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	15-17	3
β-strand	19	1	10
α-helix	28-45	18
β-strand	51-57	7	10
β-strand	64-69	6	10
α-helix	72-76	5
α-helix	81-93	13
β-strand	101-102	2	10
α-helix	112-124	13
α-helix	129-141	13
β-strand	147-154	8	11
β-strand	163-166	4	11
β-strand	169-170	2	11
β-strand	180-190	11	11
β-strand	193-204	12	11

44 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 ribosomal RNA	a	RNA	1534	Escherichia coli BW25113
30S ribosomal protein S2	b	protein	218	Escherichia coli BW25113	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	c	protein	206	Escherichia coli BW25113	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	d	protein	205	Escherichia coli BW25113	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	e	protein	157	Escherichia coli BW25113	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	f	protein	100	Escherichia coli BW25113	P02358
30S ribosomal protein S7	g	protein	161	Escherichia coli BW25113	P02359
30S ribosomal protein S8	h	protein	129	Escherichia coli BW25113	P0A7W7
30S ribosomal protein S9	i	protein	127	Escherichia coli BW25113	P0A7X3
30S ribosomal protein S10	j	protein	98	Escherichia coli BW25113	P0A7R5
30S ribosomal protein S11	k	protein	116	Escherichia coli BW25113	P0A7R9
30S ribosomal protein S12	l	protein	123	Escherichia coli BW25113	P0A7S3

45 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>6H4N_1 16S ribosomal RNA (chains a)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGG
GAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGG
GAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUU
CGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUG
ACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGG
GUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCG
UAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG
GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAA
ACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCC
UUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUU
CGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGA
AUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA
AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCC
GGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGA
CCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACU
CGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUU
CCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCAC

Sequence of entity 2 (b), FASTA

>6H4N_2 30S ribosomal protein S2 (chains b)
MLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKIL
FVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDK
LTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVD
TNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRS

Sequence of entity 3 (c), FASTA

>6H4N_3 30S ribosomal protein S3 (chains c)
GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA
KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSIT
SQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD
IDYNTSEAHTTYGVIGVKVWIFKGEI

Sequence of entity 4 (d), FASTA

>6H4N_4 30S ribosomal protein S4 (chains d)
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKV
RRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHK
AIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGT
FKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (e), FASTA

>6H4N_5 30S ribosomal protein S5 (chains e)
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARR
NMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYG
STNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILG

Sequence of entity 6 (f), FASTA

>6H4N_6 30S ribosomal protein S6 (chains f)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEAS

Sequence of entity 7 (g), FASTA

>6H4N_7 30S ribosomal protein S7 (chains g)
PRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEA
FEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLA
NELSDAAENKGTAVKKREDVHRMAEANKAFAHYAWLSLRSA

Sequence of entity 8 (h), FASTA

>6H4N_8 30S ribosomal protein S8 (chains h)
SMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELEL
TLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGL
GGEIICYVA

Sequence of entity 9 (i), FASTA

>6H4N_9 30S ribosomal protein S9 (chains i)
NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDL
YITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARR
RPQFSKR

Sequence of entity 10 (j), FASTA

>6H4N_10 30S ribosomal protein S10 (chains j)
RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQ
YEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL

Sequence of entity 11 (k), FASTA

>6H4N_11 30S ribosomal protein S11 (chains k)
RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCAD
AVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRR

Sequence of entity 12 (l), FASTA

>6H4N_12 30S ribosomal protein S12 (chains l)
ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGF
EVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKR
PKA

Primary citation

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Beckert, B., Turk, M., Czech, A. et al. Nat Microbiol (2018) 3:1115-1121. DOI 10.1038/s41564-018-0237-0 · 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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