9N2B: 30S ribosomal protein S2

Name: PDB 9N2B: Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsB ribosome (BBB-70S)
Published: 2025-03-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsB ribosome (BBB-70S). Determined by electron microscopy at 2.2 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 2.2 Å
Organisms: Escherichia coli K-12, Escherichia coli BL21
Chains: 54
Atoms: 142,763
Mol. weight: 2196.18 kDa
Ligands: FME, ATP, ZN, MG
Released: 19 Mar 2025

Explore 9N2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N2B contains 240 α-helices and 310 β-strands across 49 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 La: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	22-23	2	72
β-strand	30-31	2	73
β-strand	36-39	4	72
β-strand	46-47	2	73
β-strand	51-53	3	72
β-strand	59-61	3	72
β-strand	65-72	8	73
β-strand	77-83	7	73

Chain Lb: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	76
β-strand	24-29	6	76
β-strand	33-40	8	77
β-strand	45-52	8	77
α-helix	53-62	10
α-helix	64-74	11

Chain LB: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	83
α-helix	6-7	2
β-strand	17-19	3	83
β-strand	24	1	84
α-helix	31-33	3
β-strand	34-36	3	85
β-strand	43	1	86
β-strand	49	1	86
β-strand	54	1	87
β-strand	61-63	3	85
β-strand	65	1	84
β-strand	76-82	7	84
β-strand	91-96	6	84
β-strand	101-105	5	84
β-strand	107	1	88
β-strand	115-116	2	84
β-strand	118	1	89
β-strand	129-131	3	89
α-helix	136	1
β-strand	140-142	3	89
β-strand	144-145	2	90
β-strand	152-154	3	90
β-strand	162-168	7	89
β-strand	171-175	5	89
β-strand	181-185	5	89
β-strand	189-192	4	89
β-strand	195	1	88
α-helix	198-202	5
β-strand	204	1	83
α-helix	208-214	7
β-strand	216	1	87
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	91
β-strand	251	1	91
β-strand	267-269	3	89

Chain Lc: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-8	6
α-helix	11-34	24
α-helix	41-61	21

Chain LC: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	92
β-strand	21-28	8	92
α-helix	30-31	2
β-strand	32-38	7	93
β-strand	47-51	5	93
α-helix	62-71	10
β-strand	80-83	4	93
β-strand	95-96	2	93
α-helix	98-101	4
β-strand	106-112	7	92
α-helix	113-115	3
β-strand	117-119	3	94
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-165	3	94
β-strand	169-181	13	92
β-strand	186-190	5	92
β-strand	200-205	6	92

Chain Ld: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	78
α-helix	18-27	10
β-strand	35-38	4	78
α-helix	42-50	9
α-helix	52-54	3
β-strand	55-58	4	78

Chain LD: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	11-13	3	1
α-helix	16-19	4
α-helix	25-39	15
β-strand	42	1	2
α-helix	68-69	2
β-strand	90	1	2
α-helix	93-95	3
α-helix	98-114	17
β-strand	118-120	3	3
α-helix	131-140	10
β-strand	146-150	5	3
α-helix	155-162	8
β-strand	167-171	5	3
α-helix	177-182	6
β-strand	185-188	4	3
α-helix	190-200	11

Chain Le: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-15	6	79
β-strand	21-26	6	79
β-strand	32-33	2	79
α-helix	42-45	4
α-helix	56-64	9

41 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 (rRNA) from the rrnB operon	16	RNA	1542	Escherichia coli K-12
30S ribosomal protein S2	SB	protein	241	Escherichia coli K-12	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	SC	protein	233	Escherichia coli K-12	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	SD	protein	206	Escherichia coli K-12	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	SE	protein	167	Escherichia coli K-12	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	SF	protein	135	Escherichia coli K-12	P02358
30S ribosomal protein S7	SG	protein	179	Escherichia coli K-12	P02359
30S ribosomal protein S8	SH	protein	130	Escherichia coli K-12	P0A7W7
30S ribosomal protein S9	SI	protein	130	Escherichia coli K-12	P0A7X3
30S ribosomal protein S10	SJ	protein	103	Escherichia coli K-12	P0A7R5
Small ribosomal subunit protein uS11	SK	protein	129	Escherichia coli K-12	P0A7R9
Small ribosomal subunit protein uS12	SL	protein	124	Escherichia coli K-12	P0A7S3

42 more molecules are not listed.

Sequence of entity 1 (16), FASTA

>9N2B_1 16S ribosomal RNA (rRNA) from the rrnB operon (chains 16)
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 (SB), FASTA

>9N2B_2 30S ribosomal protein S2 (chains SB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (SC), FASTA

>9N2B_3 30S ribosomal protein S3 (chains SC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (SD), FASTA

>9N2B_4 30S ribosomal protein S4 (chains SD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (SE), FASTA

>9N2B_5 30S ribosomal protein S5 (chains SE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (SF), FASTA

>9N2B_6 30S ribosomal protein S6 (chains SF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (SG), FASTA

>9N2B_7 30S ribosomal protein S7 (chains SG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (SH), FASTA

>9N2B_8 30S ribosomal protein S8 (chains SH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (SI), FASTA

>9N2B_9 30S ribosomal protein S9 (chains SI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (SJ), FASTA

>9N2B_10 30S ribosomal protein S10 (chains SJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (SK), FASTA

>9N2B_11 Small ribosomal subunit protein uS11 (chains SK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (SL), FASTA

>9N2B_12 Small ribosomal subunit protein uS12 (chains SL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
FME	N-formylmethionine	C6 H11 N O3 S	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	276
SPD	Spermidine	C7 H19 N3	5
PUT	1,4-diaminobutane	C4 H12 N2	9

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

Primary citation

Impacts of ribosomal RNA sequence variation on gene expression and phenotype. Welfer, G.A., Brady, R.A., Natchiar, S.K. et al. Philos Trans R Soc Lond B Biol Sci (2025) 380:20230379-20230379. DOI 10.1098/rstb.2023.0379 · 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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