9FY3: Large ribosomal subunit protein bL32

Name: PDB 9FY3: Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
Published: 2026-01-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site. Determined by electron microscopy at 2.8 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Clostridioides difficile 630
Chains: 53
Atoms: 139,157
Mol. weight: 2167.44 kDa
Ligands: ZN
Released: 14 Jan 2026

Explore 9FY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FY3 contains 237 α-helices and 320 β-strands across 47 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, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-15	6
α-helix	22-25	4
β-strand	27-29	3	1
β-strand	36-38	3	1
β-strand	41	1	2

Chain 1: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
β-strand	15-21	7	7
α-helix	29-30	2
β-strand	31-36	6	7
β-strand	41-46	6	7
α-helix	47-48	2

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-23	6
α-helix	25-37	13

Chain 3: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	8-11	4
β-strand	14-16	3	12
β-strand	22-24	3	12
α-helix	33-35	3
α-helix	38-45	8
β-strand	48-49	2	12
α-helix	52-58	7
α-helix	60-62	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	17
β-strand	15-19	5	17
β-strand	22-26	5	17
α-helix	30-32	3
β-strand	34-35	2	17

Chain 5: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	82	1	22
α-helix	86-92	7
α-helix	94-95	2
α-helix	101-104	4
α-helix	108-111	4

Chain 6: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	14-16	3	25
β-strand	21-22	2	25
β-strand	31-33	3	25
α-helix	41-44	4

Chain b: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	19	1	86
α-helix	25-27	3
β-strand	31-35	5	86
β-strand	38-41	4	86
α-helix	43-63	21
β-strand	67-70	4	87
α-helix	74-76	3
α-helix	77-87	11
β-strand	90-92	3	87
α-helix	108-113	6
α-helix	143-147	5
β-strand	160-163	4	87
α-helix	170-179	10
β-strand	183-187	5	87
β-strand	198-201	4	87
α-helix	207-222	16

39 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
Large ribosomal subunit protein bL32	0	protein	59	Bacillus subtilis subsp. subtilis str. 168	O34687 (AlphaFold model)
50S ribosomal protein L33 1	1	protein	49	Bacillus subtilis subsp. subtilis str. 168	P56849 (AlphaFold model)
50S ribosomal protein L34	2	protein	44	Bacillus subtilis subsp. subtilis str. 168	P05647 (AlphaFold model)
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
Nascent Chain CliM	5	protein	38	Clostridioides difficile 630	A0A9Q7T0I1
50S ribosomal protein L31	6	protein	66	Bacillus subtilis subsp. subtilis str. 168	Q03223
5S rRNA	B	RNA	112	Bacillus subtilis subsp. subtilis str. 168
Large ribosomal subunit protein uL2	C	protein	277	Bacillus subtilis subsp. subtilis str. 168	P42919
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

41 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9FY3_1 Large ribosomal subunit protein bL32 (chains 0)
MAVPFRRTSKVKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN

Sequence of entity 2 (1), FASTA

>9FY3_2 50S ribosomal protein L33 1 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK

Sequence of entity 3 (2), FASTA

>9FY3_3 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA

Sequence of entity 4 (3), FASTA

>9FY3_4 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK

Sequence of entity 5 (4), FASTA

>9FY3_5 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG

Sequence of entity 6 (5), FASTA

>9FY3_6 Nascent Chain CliM (chains 5)
YVLIRDIFVNRITYSEERLPKQYIVFQKYDIWRYCSLF

Sequence of entity 7 (6), FASTA

>9FY3_7 50S ribosomal protein L31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYGLK

Sequence of entity 8 (B), FASTA

>9FY3_8 5S rRNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA

Sequence of entity 9 (C), FASTA

>9FY3_9 Large ribosomal subunit protein uL2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGVRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 10 (D), FASTA

>9FY3_10 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 11 (E), FASTA

>9FY3_11 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 12 (F), FASTA

>9FY3_12 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Diverse mechanisms of translation arrest by a Clostridia ribosome stalling peptide CliM. Yoshida, M., Gersteuer, F., Berendes, O. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-72673-5 · PubMed

Other PDB entries of the same protein (UniProt O34687 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8S1P 1.96 Å, YlmH bound to PtRNA-50S
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
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)
7SAE 3.0 Å, 44SR70P Class1 ribosomal particle
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)

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