4V9C: 30S ribosomal protein S2

Allosteric control of the ribosome by small-molecule antibiotics. Determined by X-ray diffraction at 3.3 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Escherichia coli
Chains: 109
Atoms: 293,103
Mol. weight: 4402.45 kDa
Ligands: ZN, NMY, MG
Released: 9 Jul 2014

Explore 4V9C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9C contains 418 α-helices and 638 β-strands across 99 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	25-30	6
α-helix	47-50	4
β-strand	69-70	2	6
α-helix	78-80	3
β-strand	86	1	7
β-strand	89	1	7
β-strand	91-92	2	6
α-helix	104-116	13
α-helix	132-141	10
α-helix	144-146	3
β-strand	162	1	6
β-strand	165	1	8
α-helix	166-169	4
α-helix	174-177	4
β-strand	184-186	3	8
β-strand	198-200	3	8
α-helix	209-218	10

Chain AC: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	12-15	4
β-strand	20	1	16
α-helix	30-37	8
α-helix	40-46	7
β-strand	57	1	16
α-helix	84-91	8
α-helix	92-96	5
α-helix	113-125	13
α-helix	132-142	11
β-strand	149-152	4	17
β-strand	167-170	4	17
β-strand	182-189	8	17
β-strand	196-203	8	17

Chain AD: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	53-60	8
α-helix	62-65	4
α-helix	69-81	13
α-helix	86-89	4
α-helix	113-119	7
α-helix	155-160	6
α-helix	200-203	4

Chain AE: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	13-21	9	41
β-strand	32-39	8	41
β-strand	47-49	3	41
β-strand	53	1	41
α-helix	56-68	13
β-strand	85-87	3	42
β-strand	94-96	3	42
β-strand	97	1	43
β-strand	106	1	43
α-helix	112-115	4
α-helix	116-118	3
β-strand	124	1	43
α-helix	133-136	4
α-helix	141-143	3

Chain AF: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	55
β-strand	10	1	56
α-helix	12-14	3
α-helix	17-23	7
α-helix	26-29	4
β-strand	40-45	6	56
β-strand	57-61	5	56
α-helix	68-76	9
α-helix	78-80	3
β-strand	87-89	3	55

Chain AG: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	32	1	66
β-strand	35	1	66
α-helix	36-50	15
α-helix	63-69	7
β-strand	73	1	67
β-strand	78	1	68
β-strand	85	1	68
β-strand	90	1	67
α-helix	91-92	2
α-helix	95-110	16
α-helix	116-128	13
α-helix	138-148	11

Chain AH: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	24-26	3	83
β-strand	48	1	83
β-strand	60-62	3	83
α-helix	63-64	2
β-strand	77	1	84
α-helix	92-94	3
α-helix	113-115	3
α-helix	116-120	5
β-strand	127	1	84

Chain AI: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	94
β-strand	11	1	94
β-strand	15-21	7	94
β-strand	22	1	95
β-strand	30	1	94
β-strand	33	1	94
β-strand	62	1	95
β-strand	65-69	5	94
α-helix	73-86	14
α-helix	96-99	4

91 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	AA, CA	RNA	1542	Escherichia coli
30S ribosomal protein S2	AB, CB	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	AG, CG	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	AH, CH	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI, CI	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ, CJ	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK, CK	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL, CL	protein	124	Escherichia coli	P0A7S3

43 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V9C_1 16S ribosomal RNA (chains AA, CA)
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 (AB, CB), FASTA

>4V9C_2 30S ribosomal protein S2 (chains AB, CB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (AC, CC), FASTA

>4V9C_3 30S ribosomal protein S3 (chains AC, CC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (AD, CD), FASTA

>4V9C_4 30S ribosomal protein S4 (chains AD, CD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE, CE), FASTA

>4V9C_5 30S ribosomal protein S5 (chains AE, CE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (AF, CF), FASTA

>4V9C_6 30S ribosomal protein S6 (chains AF, CF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (AG, CG), FASTA

>4V9C_7 30S ribosomal protein S7 (chains AG, CG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (AH, CH), FASTA

>4V9C_8 30S ribosomal protein S8 (chains AH, CH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (AI, CI), FASTA

>4V9C_9 30S ribosomal protein S9 (chains AI, CI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V9C_10 30S ribosomal protein S10 (chains AJ, CJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (AK, CK), FASTA

>4V9C_11 30S ribosomal protein S11 (chains AK, CK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (AL, CL), FASTA

>4V9C_12 30S ribosomal protein S12 (chains AL, CL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NMY	Neomycin	C23 H46 N6 O13	18
MG	Magnesium ion	Mg	490

Primary citation

Allosteric control of the ribosome by small-molecule antibiotics. Wang, L., Pulk, A., Wasserman, M.R. et al. Nat Struct Mol Biol (2012) 19:957-963. DOI 10.1038/nsmb.2360 · 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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