7O1C: 30S ribosomal protein S2

Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome-RF2 complex stalled in response to L-tryptophan. Determined by electron microscopy at 2.6 Å resolution. Released 1 Sept 2021.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Escherichia coli K-12, Escherichia coli (strain K12)
Chains: 56
Atoms: 148,175
Mol. weight: 2221.66 kDa
Ligands: MG, ZN, TRP
Released: 1 Sept 2021

Explore 7O1C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O1C contains 252 α-helices and 316 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 AB: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	4
α-helix	25-27	3
β-strand	31-35	5	4
β-strand	38-41	4	4
α-helix	43-62	20
β-strand	67-70	4	5
α-helix	79-85	7
β-strand	90-92	3	5
α-helix	104-121	18
α-helix	134-148	15
β-strand	160-164	5	5
α-helix	170-177	8
β-strand	183-187	5	5
β-strand	198-201	4	5
α-helix	207-222	16

Chain AC: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	12	1	11
β-strand	16	1	11
β-strand	20	1	12
α-helix	26-46	21
α-helix	48-50	3
β-strand	52-58	7	12
β-strand	64-70	7	12
α-helix	73-77	5
α-helix	84-95	12
β-strand	99-105	7	12
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-142	13
β-strand	148-154	7	13
α-helix	157-159	3
β-strand	165-170	6	13
β-strand	182-191	10	13
β-strand	194-203	10	13

Chain AD: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	28-31	4
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-95	10
β-strand	97	1	18
α-helix	98-104	7
α-helix	111-119	9
β-strand	123-125	3	19
β-strand	128-129	2	19
α-helix	135	1
β-strand	136	1	18
α-helix	137-138	2
β-strand	142-145	4	19
α-helix	147-149	3
α-helix	153-161	9
α-helix	166-168	3
β-strand	172-174	3	19
β-strand	179-181	3	19
α-helix	185-187	3
α-helix	197-203	7

Chain AE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-24	13	23
β-strand	29-40	12	23
β-strand	45-53	9	23
α-helix	56-68	13
β-strand	72-73	2	23
β-strand	80	1	24
β-strand	85-89	5	25
β-strand	92-98	7	25
β-strand	105-106	2	25
α-helix	111-118	8
β-strand	122	1	24
β-strand	123-129	7	25
α-helix	133-145	13
α-helix	150-157	8

Chain AF: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	29
α-helix	12-17	6
α-helix	18-31	14
β-strand	35-45	11	29
β-strand	57-66	10	29
α-helix	68-80	13
β-strand	84-92	9	29
α-helix	99-100	2
α-helix	101-104	4

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-66	9
β-strand	73-79	7	35
β-strand	84-90	7	35
α-helix	91-92	2
α-helix	93-107	15
α-helix	116-128	13
α-helix	133-147	15
α-helix	149-151	3

Chain AH: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	39
α-helix	31-42	12
β-strand	49-52	4	39
β-strand	58-62	5	39
β-strand	65	1	40
β-strand	70	1	40
β-strand	75-77	3	41
β-strand	86-87	2	41
α-helix	95-98	4
β-strand	101-106	6	41
β-strand	109-112	4	41
α-helix	115-118	4
β-strand	123-129	7	41

Chain AI: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	44
β-strand	16-23	8	44
β-strand	27-30	4	44
β-strand	33-34	2	44
α-helix	35-38	4
α-helix	42-54	13
β-strand	61-68	8	44
α-helix	72-91	20
α-helix	95-100	6
α-helix	111-114	4
α-helix	124-126	3

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
Ribosomal RNA 16S	AA	RNA	1534	Escherichia coli K-12
30S ribosomal protein S2	AB	protein	241	Escherichia coli (strain K12)	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC	protein	233	Escherichia coli (strain K12)	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD	protein	206	Escherichia coli (strain K12)	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE	protein	167	Escherichia coli (strain K12)	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF	protein	135	Escherichia coli (strain K12)	P02358
30S ribosomal protein S7	AG	protein	179	Escherichia coli (strain K12)	P02359
30S ribosomal protein S8	AH	protein	130	Escherichia coli (strain K12)	P0A7W7
30S ribosomal protein S9	AI	protein	130	Escherichia coli (strain K12)	P0A7X3
30S ribosomal protein S10	AJ	protein	103	Escherichia coli (strain K12)	P0A7R5
30S ribosomal protein S11	AK	protein	129	Escherichia coli (strain K12)	P0A7R9
30S ribosomal protein S12	AL	protein	124	Escherichia coli (strain K12)	P0A7S3

44 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>7O1C_1 Ribosomal RNA 16S (chains AA)
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
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA

Sequence of entity 2 (AB), FASTA

>7O1C_2 30S ribosomal protein S2 (chains AB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (AC), FASTA

>7O1C_3 30S ribosomal protein S3 (chains AC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (AD), FASTA

>7O1C_4 30S ribosomal protein S4 (chains AD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE), FASTA

>7O1C_5 30S ribosomal protein S5 (chains AE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (AF), FASTA

>7O1C_6 30S ribosomal protein S6 (chains AF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (AG), FASTA

>7O1C_7 30S ribosomal protein S7 (chains AG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (AH), FASTA

>7O1C_8 30S ribosomal protein S8 (chains AH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (AI), FASTA

>7O1C_9 30S ribosomal protein S9 (chains AI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (AJ), FASTA

>7O1C_10 30S ribosomal protein S10 (chains AJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (AK), FASTA

>7O1C_11 30S ribosomal protein S11 (chains AK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (AL), FASTA

>7O1C_12 30S ribosomal protein S12 (chains AL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	339
ZN	Zinc ion	Zn	3
TRP	Tryptophan	C11 H12 N2 O2	1

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

Primary citation

Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling. van der Stel, A.X., Gordon, E.R., Sengupta, A. et al. Nat Commun (2021) 12:5340-5340. DOI 10.1038/s41467-021-25663-8 · 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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