4WOI: 30S ribosomal protein S2

Name: PDB 4WOI: 4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2
Published: 2015-08-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2. Determined by X-ray diffraction at 3.0 Å resolution. Released 5 Aug 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Escherichia coli str. K-12 substr. MDS42, Escherichia coli, Enterobacteria phage L1
Chains: 110
Atoms: 294,034
Mol. weight: 4419.08 kDa
Ligands: ZN, PAR, MG
Released: 5 Aug 2015

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

Secondary structure: helices and β-sheets

4WOI contains 432 α-helices and 636 β-strands across 100 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: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	43-46	4
β-strand	69-70	2	13
α-helix	77-79	3
α-helix	83-85	3
α-helix	108-118	11
α-helix	133-145	13
β-strand	162-165	4	13
α-helix	170-179	10
β-strand	185-186	2	13
β-strand	199	1	13
α-helix	207-221	15

Chain AC: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20-21	2	23
α-helix	27-34	8
α-helix	36-42	7
β-strand	52-55	4	24
β-strand	57-58	2	23
β-strand	64	1	25
β-strand	65	1	23
β-strand	68-70	3	24
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-93	12
β-strand	99	1	25
β-strand	103-105	3	24
α-helix	113-124	12
α-helix	130-142	13
β-strand	148-152	5	26
β-strand	167-171	5	26
β-strand	181-188	8	26
β-strand	197-205	9	26

Chain AD: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
α-helix	50-55	6
α-helix	61-64	4
α-helix	69-80	12
α-helix	86-89	4
α-helix	91-94	4
β-strand	97	1	30
α-helix	100-103	4
β-strand	123-124	2	31
β-strand	129	1	31
β-strand	136	1	30
β-strand	144-145	2	31
α-helix	147-149	3
α-helix	185-187	3
α-helix	197-204	8

Chain AE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	13-21	9	38
β-strand	25	1	39
β-strand	28	1	39
β-strand	32-40	9	38
β-strand	46-53	8	38
α-helix	57-68	12
β-strand	72	1	38
β-strand	85-89	5	40
β-strand	92-97	6	40
β-strand	106	1	40
α-helix	109-116	8
β-strand	124-129	6	40
α-helix	133-144	12
α-helix	153-156	4

Chain AF: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	48
β-strand	6	1	49
β-strand	9-10	2	50
α-helix	12-14	3
α-helix	20-29	10
β-strand	40-41	2	51
β-strand	58-59	2	50
β-strand	60-61	2	51
β-strand	65-66	2	48
α-helix	71-74	4
β-strand	84-86	3	50
β-strand	89	1	49

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	44-50	7
α-helix	59-61	3
α-helix	63-65	3
β-strand	73-75	3	59
β-strand	88-90	3	59
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-125	10
α-helix	134-146	13

Chain AH: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
β-strand	24	1	70
α-helix	31-41	11
β-strand	49-50	2	71
β-strand	60-61	2	71
β-strand	62	1	70
β-strand	65-66	2	72
β-strand	69-70	2	72
β-strand	75-77	3	73
β-strand	80	1	74
β-strand	83	1	74
β-strand	86	1	75
α-helix	95-98	4
β-strand	101-104	4	73
β-strand	112	1	73
α-helix	113-119	7
β-strand	124	1	75
β-strand	125-129	5	73

Chain AI: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	85
β-strand	16-20	5	85
β-strand	22-25	4	86
β-strand	28-30	3	87
β-strand	33-34	2	87
α-helix	35-39	5
α-helix	45-49	5
α-helix	50-52	3
β-strand	61-62	2	86
β-strand	63-64	2	87
β-strand	65-68	4	85
α-helix	72-86	15
α-helix	97-100	4
α-helix	111-114	4
α-helix	124-126	3

92 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, DA	RNA	1542	Escherichia coli str. K-12 substr. MDS42
30S ribosomal protein S2	AB, DB	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC, DC	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD, DD	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE, DE	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF, DF	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	AG, DG	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	AH, DH	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI, DI	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ, DJ	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK, DK	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL, DL	protein	124	Escherichia coli	P0A7S3

44 more molecules are not listed.

Sequence of entity 1 (AA, DA), FASTA

>4WOI_1 16S ribosomal RNA (chains AA, DA)
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, DB), FASTA

>4WOI_2 30S ribosomal protein S2 (chains AB, DB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (AC, DC), FASTA

>4WOI_3 30S ribosomal protein S3 (chains AC, DC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (AD, DD), FASTA

>4WOI_4 30S ribosomal protein S4 (chains AD, DD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE, DE), FASTA

>4WOI_5 30S ribosomal protein S5 (chains AE, DE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (AF, DF), FASTA

>4WOI_6 30S ribosomal protein S6 (chains AF, DF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (AG, DG), FASTA

>4WOI_7 30S ribosomal protein S7 (chains AG, DG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (AH, DH), FASTA

>4WOI_8 30S ribosomal protein S8 (chains AH, DH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (AI, DI), FASTA

>4WOI_9 30S ribosomal protein S9 (chains AI, DI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (AJ, DJ), FASTA

>4WOI_10 30S ribosomal protein S10 (chains AJ, DJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (AK, DK), FASTA

>4WOI_11 30S ribosomal protein S11 (chains AK, DK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (AL, DL), FASTA

>4WOI_12 30S ribosomal protein S12 (chains AL, DL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
PAR	Paromomycin	C23 H45 N5 O14	13
MG	Magnesium ion	Mg	495

Primary citation

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions. Wasserman, M.R., Pulk, A., Zhou, Z. et al. Nat Commun (2015) 6:7896-7896. DOI 10.1038/ncomms8896 · 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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