8S1P: YlmH

Name: PDB 8S1P: YlmH bound to PtRNA-50S
Published: 2024-06-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

YlmH bound to PtRNA-50S. Determined by electron microscopy at 1.96 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 1.96 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 32
Atoms: 91,097
Mol. weight: 1392.94 kDa
Ligands: MG, CLM, ZN
Released: 12 Jun 2024

Explore 8S1P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S1P contains 153 α-helices and 216 β-strands across 28 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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	22-25	4
β-strand	27-29	3	10
β-strand	36-38	3	10
β-strand	41	1	47
β-strand	48	1	11
β-strand	53	1	11

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	12
β-strand	15-22	8	12
α-helix	29-30	2
β-strand	31-36	6	12
β-strand	41-47	7	12

Chain 2: 3 helices, 0 β-strands

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

Chain 3: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	1
α-helix	21	1
β-strand	22-24	3	1
α-helix	33-35	3
α-helix	38-45	8
β-strand	48-49	2	1
α-helix	50-51	2
α-helix	52-58	7
α-helix	59-62	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	15-19	5	2
β-strand	22-26	5	2
α-helix	30-32	3
β-strand	34-36	3	2

Chain 6: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	9
β-strand	21-26	6	9
β-strand	30-33	4	9

Chain C: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
α-helix	6-7	2
β-strand	17-19	3	13
α-helix	31-33	3
β-strand	34-35	2	14
β-strand	43	1	15
β-strand	49	1	15
β-strand	54	1	16
α-helix	61	1
β-strand	62-63	2	14
β-strand	65	1	17
β-strand	72	1	18
β-strand	76-82	7	17
β-strand	91-96	6	17
β-strand	101-105	5	17
β-strand	107	1	19
β-strand	115-116	2	17
β-strand	118	1	18
β-strand	129-131	3	18
α-helix	136	1
β-strand	140-142	3	18
β-strand	144	1	20
β-strand	154	1	20
β-strand	162-168	7	18
β-strand	171-175	5	18
β-strand	181-185	5	18
β-strand	189-192	4	18
β-strand	195	1	19
α-helix	198-202	5
α-helix	208-213	6
β-strand	216	1	16
α-helix	217-221	5
α-helix	222-224	3
β-strand	247	1	21
β-strand	253	1	21
α-helix	265-268	4
β-strand	270-272	3	18

Chain D: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	22
β-strand	22-29	8	22
α-helix	31-32	2
β-strand	33-39	7	23
β-strand	48-55	8	23
α-helix	56-57	2
α-helix	63-68	6
β-strand	77-84	8	23
α-helix	88-90	3
β-strand	96-97	2	23
α-helix	99-101	3
β-strand	107-113	7	22
α-helix	114-116	3
β-strand	118-120	3	24
α-helix	122-126	5
α-helix	128-130	3
α-helix	154-155	2
β-strand	162-164	3	24
β-strand	168-180	13	22
β-strand	185-189	5	22
β-strand	199-204	6	22

20 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
50S ribosomal protein L35	3	protein	66	Bacillus subtilis subsp. subtilis str. 168	P55874 (AlphaFold model)
50S ribosomal protein L36	4	protein	37	Bacillus subtilis subsp. subtilis str. 168	P20278 (AlphaFold model)
50S ribosomal protein L31	6	protein	66	Bacillus subtilis subsp. subtilis str. 168	Q03223 (AlphaFold model)
23S rRNA	A	RNA	2928	Bacillus subtilis subsp. subtilis str. 168
5S rRNA	B	RNA	112	Bacillus subtilis subsp. subtilis str. 168
50S ribosomal protein L2	C	protein	277	Bacillus subtilis subsp. subtilis str. 168	P42919 (AlphaFold model)
50S ribosomal protein L3	D	protein	209	Bacillus subtilis subsp. subtilis str. 168	P42920
50S ribosomal protein L4	E	protein	207	Bacillus subtilis subsp. subtilis str. 168	P42921
50S ribosomal protein L5	F	protein	179	Bacillus subtilis subsp. subtilis str. 168	P12877
Large ribosomal subunit protein uL6	G	protein	179	Bacillus subtilis subsp. subtilis str. 168	P46898
50S ribosomal protein L13	J	protein	145	Bacillus subtilis subsp. subtilis str. 168	P70974
50S ribosomal protein L14	K	protein	122	Bacillus subtilis subsp. subtilis str. 168	P12875

20 more molecules are not listed.

Sequence of entity 1 (3), FASTA

>8S1P_1 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK

Sequence of entity 2 (4), FASTA

>8S1P_2 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG

Sequence of entity 3 (6), FASTA

>8S1P_3 50S ribosomal protein L31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYGLK

Sequence of entity 4 (A), FASTA

>8S1P_4 23S rRNA (chains A)
GGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGG
ACGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUG
GGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAG
GCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCC
CUGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUG
UAGGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCC
GCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGU
ACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUAC
UCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGG
GGAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGA
UGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCUCGUGCAAGGUUAAGCAGAAG
AUGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCC
GAAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCG
AACCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGA
ACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCU
UGGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACU
CCGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAA
AGGGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUG
UGGAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGU
AAUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCG
AAGCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGA
CCGGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGG
UGAGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUU
AGUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUG
UACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAU
UGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGGCU
GAGCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAA
GCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAA
UCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCG
GGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGC
GACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACG
CCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAG
CCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGU
AAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGU
GAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGA
GCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUU
GGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGA
CCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGG
GGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAA
UCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGG
GACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAU
AAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGU
UUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGC
UGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCC
CUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGA
UGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCG
GACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAU
UCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGU
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCAU

Sequence of entity 5 (B), FASTA

>8S1P_5 5S rRNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA

Sequence of entity 6 (C), FASTA

>8S1P_6 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 7 (D), FASTA

>8S1P_7 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 8 (E), FASTA

>8S1P_8 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 9 (F), FASTA

>8S1P_9 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Sequence of entity 10 (G), FASTA

>8S1P_10 Large ribosomal subunit protein uL6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK

Sequence of entity 11 (J), FASTA

>8S1P_11 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG

Sequence of entity 12 (K), FASTA

>8S1P_12 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	158
CLM	Chloramphenicol	C11 H12 Cl2 N2 O5	1
ZN	Zinc ion	Zn	4

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

Primary citation

A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. Takada, H., Paternoga, H., Fujiwara, K. et al. Nucleic Acids Res (2024) 52:8483-8499. DOI 10.1093/nar/gkae399 · PubMed

Other PDB entries of the same protein (UniProt P55874 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QCQ 2.3 Å, B. subtilis ApdA-stalled ribosomal complex
9FY1 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in…
9FY2 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
9FY3 2.8 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
7AS8 2.9 Å, Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with…
8BUU 2.9 Å, ARE-ABCF VmlR2 bound to a 70S ribosome
7AQC 2.99 Å, Structure of the bacterial RQC complex (Decoding State)
6TNN 3.07 Å, Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA
6TPQ 3.07 Å, RNase M5 bound to 50S ribosome with precursor 5S rRNA
6HA1 3.1 Å, Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader…
7AQD 3.1 Å, Structure of the bacterial RQC complex (Translocating State)
7OPE 3.2 Å, RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)

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