8CAI: Streptomycin and Hygromycin B

Name: PDB 8CAI: Streptomycin and Hygromycin B bound to the 30S body
Published: 2023-07-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Streptomycin and Hygromycin B bound to the 30S body. Determined by electron microscopy at 2.08 Å resolution. Released 26 Jul 2023.

Method: Electron microscopy
Resolution: 2.08 Å
Organism: Escherichia coli BW25113
Chains: 15
Atoms: 37,814
Mol. weight: 711.69 kDa
Ligands: HY0, 5I0, SCM, MG
Released: 26 Jul 2023

Explore 8CAI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CAI contains 66 α-helices and 70 β-strands across 14 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 B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	1
α-helix	25-30	6
β-strand	33-34	2	1
β-strand	38-40	3	1
α-helix	43-61	19
β-strand	67-70	4	2
α-helix	77-87	11
β-strand	90-92	3	2
α-helix	104-121	18
α-helix	139-148	10
β-strand	160-164	5	2
α-helix	170-179	10
β-strand	183-187	5	2
β-strand	198-201	4	2
α-helix	207-225	19

Chain C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	124-126	3
α-helix	130-134	5
β-strand	148-155	8	3
β-strand	164-171	8	3
β-strand	188-190	3	3
β-strand	195-200	6	3

Chain D: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	28-31	4
α-helix	37	1
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-95	10
β-strand	97	1	4
α-helix	98-105	8
α-helix	111-119	9
β-strand	123-125	3	5
β-strand	128-129	2	5
β-strand	136	1	4
β-strand	141-145	5	5
α-helix	147-149	3
α-helix	153-164	12
α-helix	166-168	3
β-strand	171-174	4	5
β-strand	179-182	4	5
α-helix	185-187	3
α-helix	198-203	6

Chain E: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-25	14	6
β-strand	28-40	13	6
β-strand	45-53	9	6
α-helix	56-69	14
β-strand	72-73	2	6
β-strand	77	1	7
β-strand	80	1	7
β-strand	85-89	5	8
β-strand	92-98	7	8
β-strand	105-106	2	8
α-helix	110-117	8
β-strand	123-129	7	8
α-helix	133-145	13
α-helix	150-157	8

Chain F: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	9
α-helix	12-17	6
α-helix	18-31	14
β-strand	35-51	17	9
β-strand	54-66	13	9
α-helix	68-80	13
β-strand	84-92	9	9
α-helix	99-100	2

Chain H: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	10
α-helix	31-42	12
β-strand	46-52	7	10
β-strand	58-63	6	10
α-helix	64	1
β-strand	65	1	11
β-strand	70	1	11
β-strand	75-77	3	12
β-strand	80	1	13
β-strand	83	1	13
β-strand	86-87	2	12
α-helix	89-91	3
α-helix	92-94	3
β-strand	101-106	6	12
β-strand	109-112	4	12
α-helix	113-119	7
β-strand	123-129	7	12

Chain K: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-25	8	14
β-strand	30-36	7	14
β-strand	41-46	6	14
α-helix	60-71	12
β-strand	81-87	7	14
α-helix	95-101	7
β-strand	106-112	7	14
α-helix	121-124	4
β-strand	125	1	15
α-helix	126-127	2

Chain L: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	22-24	3
β-strand	29-40	12	16
α-helix	41-43	3
β-strand	50-57	8	16
β-strand	62-66	5	16
β-strand	79-84	6	16
β-strand	93-97	5	16
α-helix	104-107	4
α-helix	114-116	3

6 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 rRNA	A	RNA	1540	Escherichia coli BW25113
30S ribosomal protein S2	B	protein	241	Escherichia coli BW25113	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli BW25113	P0A7V3 (AlphaFold model)
Small ribosomal subunit protein uS4	D	protein	206	Escherichia coli BW25113	P0A7V8 (AlphaFold model)
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli BW25113	P0A7W1 (AlphaFold model)
Small ribosomal subunit protein bS6, non-modified isoform	F	protein	131	Escherichia coli BW25113	P02358
Small ribosomal subunit protein uS8	H	protein	130	Escherichia coli BW25113	P0A7W7
Small ribosomal subunit protein uS11	K	protein	129	Escherichia coli BW25113	P0A7R9
Small ribosomal subunit protein uS12	L	protein	124	Escherichia coli BW25113	P0A7S3
Small ribosomal subunit protein uS15	O	protein	89	Escherichia coli BW25113	P0ADZ4
30S ribosomal protein S16	P	protein	82	Escherichia coli BW25113	P0A7T3
Small ribosomal subunit protein uS17	Q	protein	84	Escherichia coli BW25113	P0AG63

3 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8CAI_1 16S rRNA (chains A)
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
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Sequence of entity 2 (B), FASTA

>8CAI_2 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (C), FASTA

>8CAI_3 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (D), FASTA

>8CAI_4 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (E), FASTA

>8CAI_5 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (F), FASTA

>8CAI_6 Small ribosomal subunit protein bS6, non-modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEE

Sequence of entity 7 (H), FASTA

>8CAI_7 Small ribosomal subunit protein uS8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 8 (K), FASTA

>8CAI_8 Small ribosomal subunit protein uS11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 9 (L), FASTA

>8CAI_9 Small ribosomal subunit protein uS12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Sequence of entity 10 (O), FASTA

>8CAI_10 Small ribosomal subunit protein uS15 (chains O)
MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMV
SQRRKLLDYLKRKDVARYTQLIERLGLRR

Sequence of entity 11 (P), FASTA

>8CAI_11 30S ribosomal protein S16 (chains P)
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHW
VGQGATISDRVAALIKEVNKAA

Sequence of entity 12 (Q), FASTA

>8CAI_12 Small ribosomal subunit protein uS17 (chains Q)
MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVE
IRECRPLSKTKSWTLVRVVEKAVL

Ligands and cofactors

ID	Name	Formula	Copies
HY0	Hygromycin B variant	C20 H37 N3 O13	3
5I0	[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3…	C21 H44 N7 O13	1
SCM	Spectinomycin	C14 H24 N2 O7	1
MG	Magnesium ion	Mg	55

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

Primary citation

Structural conservation of antibiotic interaction with ribosomes. Paternoga, H., Crowe-McAuliffe, C., Bock, L.V. et al. Nat Struct Mol Biol (2023) 30:1380-1392. DOI 10.1038/s41594-023-01047-y · 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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