9Q87: Small ribosomal subunit protein uS2

Name: PDB 9Q87: Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+
Published: 2025-05-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+. Determined by electron microscopy at 1.55 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 1.55 Å
Organism: Escherichia coli B
Chains: 55
Atoms: 166,869
Mol. weight: 2198.62 kDa
Ligands: MG, CU1, ZN
Released: 14 May 2025

Explore 9Q87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q87 contains 268 α-helices and 302 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 0: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	88
β-strand	20-25	6	88
α-helix	33-34	2
β-strand	35-40	6	88
β-strand	45-52	8	88

Chain 1: 3 helices, 0 β-strands

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

Chain 2: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	14-16	3	92
β-strand	22-24	3	92
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	92
α-helix	50-51	2
α-helix	52-61	10

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	14-19	6	1
β-strand	22-27	6	1
α-helix	31-33	3
β-strand	35-37	3	1

Chain 5: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	35-48	14
α-helix	57-59	3
α-helix	79-81	3
α-helix	103-110	8
α-helix	111-113	3
α-helix	122-125	4
α-helix	126-136	11

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	2
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-35	5	2
β-strand	38-41	4	2
α-helix	43-62	20
β-strand	67-70	4	3
α-helix	77-87	11
β-strand	90-92	3	3
α-helix	95-97	3
α-helix	104-123	20
α-helix	125-128	4
α-helix	132-148	17
α-helix	149-151	3
β-strand	160-164	5	3
α-helix	170-179	10
β-strand	183-187	5	3
β-strand	198-201	4	3
α-helix	207-228	22

Chain c: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	14
α-helix	6-7	2
β-strand	17-19	3	14
β-strand	24	1	15
α-helix	31-33	3
β-strand	34-35	2	16
β-strand	43	1	17
β-strand	49	1	17
β-strand	54	1	18
α-helix	61	1
β-strand	62-63	2	16
β-strand	76-82	7	15
β-strand	91-96	6	15
β-strand	101-105	5	15
α-helix	106	1
β-strand	107	1	19
β-strand	115-116	2	15
β-strand	118	1	20
β-strand	129-131	3	20
α-helix	132-134	3
β-strand	140-142	3	20
β-strand	144-145	2	21
β-strand	152-154	3	21
β-strand	162-168	7	20
β-strand	171-175	5	20
β-strand	181-185	5	20
β-strand	189-192	4	20
β-strand	195	1	19
α-helix	198-202	5
β-strand	204	1	14
α-helix	208-212	5
β-strand	216	1	18
α-helix	217-219	3
α-helix	222-224	3
β-strand	245	1	22
β-strand	251	1	22
α-helix	264-266	3
β-strand	267-269	3	20

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20-21	2	5
α-helix	26-46	21
β-strand	52-58	7	5
β-strand	64-70	7	5
α-helix	73-77	5
α-helix	79-81	3
α-helix	82-95	14
β-strand	99-105	7	5
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-155	8	6
α-helix	157-159	3
β-strand	164-171	8	6
β-strand	180-191	12	6
β-strand	194-206	13	6

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
30S	A	RNA	1554	Escherichia coli B
Small ribosomal subunit protein uS2	B	protein	233	Escherichia coli B	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli B	P0A7V3 (AlphaFold model)
Small ribosomal subunit protein uS4	D	protein	206	Escherichia coli B	P0A7V8 (AlphaFold model)
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli B	P0A7W1 (AlphaFold model)
Small ribosomal subunit protein bS6, fully modified isoform	F	protein	135	Escherichia coli B	P02358
Small ribosomal subunit protein uS7	G	protein	179	Escherichia coli B	P02359
Small ribosomal subunit protein uS8	H	protein	130	Escherichia coli B	P0A7W7
Small ribosomal subunit protein uS9	I	protein	130	Escherichia coli B	P0A7X3
Small ribosomal subunit protein uS10	J	protein	103	Escherichia coli B	P0A7R5
Small ribosomal subunit protein uS11	K	protein	129	Escherichia coli B	P0A7R9
Small ribosomal subunit protein uS12	L	protein	124	Escherichia coli B	P0A7S3

43 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9Q87_1 30S (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGCAGCUUGCUGCUUCGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUAGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUACCUUAAAGAAGC

Sequence of entity 2 (B), FASTA

>9Q87_2 Small ribosomal subunit protein uS2 (chains B)
ATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIA
SRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQS
QDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGI
PVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQLASQAEE

Sequence of entity 3 (C), FASTA

>9Q87_3 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (D), FASTA

>9Q87_4 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (E), FASTA

>9Q87_5 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (F), FASTA

>9Q87_6 Small ribosomal subunit protein bS6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (G), FASTA

>9Q87_7 Small ribosomal subunit protein uS7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (H), FASTA

>9Q87_8 Small ribosomal subunit protein uS8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (I), FASTA

>9Q87_9 Small ribosomal subunit protein uS9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (J), FASTA

>9Q87_10 Small ribosomal subunit protein uS10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (K), FASTA

>9Q87_11 Small ribosomal subunit protein uS11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (L), FASTA

>9Q87_12 Small ribosomal subunit protein uS12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	415
CU1	Copper (I) ion	Cu	5
ZN	Zinc ion	Zn	1

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

Primary citation

Principles of ion binding to RNA inferred from the analysis of a 1.55 angstrom resolution bacterial ribosome structure - Part I: Mg2. Leonarski, F., Henning-Knechtel, A., Kirmizialtin, S. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkae1148 · 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)
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
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain

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