7QV2: Bacillus subtilis collided disome

Name: PDB 7QV2: Bacillus subtilis collided disome (Collided 70S)
Published: 2022-03-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Bacillus subtilis collided disome (Collided 70S). Determined by electron microscopy at 3.5 Å resolution. Released 9 Mar 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 53
Atoms: 142,856
Mol. weight: 2165.66 kDa
Released: 9 Mar 2022

Explore 7QV2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QV2 contains 230 α-helices and 292 β-strands across 46 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
α-helix	23-26	4
β-strand	27-29	3	1
β-strand	36-38	3	1
β-strand	49	1	2
β-strand	52	1	2

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	17-22	6	8
α-helix	29-30	2
β-strand	31-36	6	8
β-strand	41-47	7	8

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-36	12

Chain 3: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	12
α-helix	18-20	3
α-helix	21	1
β-strand	22-25	4	12
α-helix	33-35	3
α-helix	38-44	7
β-strand	47-49	3	12
α-helix	52-58	7

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	13
β-strand	15-19	5	13
β-strand	22-26	5	13
α-helix	30-32	3
β-strand	34-35	2	13

Chain 6: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
β-strand	6	1	15
α-helix	7-8	2
β-strand	10-14	5	16
β-strand	22-27	6	16
β-strand	30-31	2	16
α-helix	49-53	5

Chain b: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	25-30	6
β-strand	31	1	17
β-strand	34	1	18
β-strand	38	1	18
β-strand	41	1	17
α-helix	43-62	20
α-helix	67	1
β-strand	68-70	3	19
α-helix	74-87	14
β-strand	91-92	2	19
α-helix	104-123	20
α-helix	132	1
α-helix	133-137	5
α-helix	138-148	11
α-helix	149-151	3
β-strand	161-163	3	19
α-helix	170-178	9
β-strand	183-185	3	19
β-strand	187	1	20
β-strand	198	1	19
β-strand	201	1	20
α-helix	207-222	16
α-helix	223-225	3

Chain c: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	21
β-strand	16	1	21
α-helix	17-18	2
β-strand	20-21	2	22
α-helix	28-46	19
α-helix	47-49	3
β-strand	53-58	6	22
β-strand	62-68	7	22
α-helix	72-76	5
α-helix	80-94	15
β-strand	97-103	7	22
α-helix	108-110	3
α-helix	112-124	13
α-helix	129-144	16
β-strand	147-154	8	23
β-strand	163-170	8	23
β-strand	181-189	9	23
β-strand	194-202	9	23

38 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 L32	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
50S ribosomal protein L31	6	protein	66	Bacillus subtilis subsp. subtilis str. 168	Q03223
mRNA	A	RNA	29	Bacillus subtilis subsp. subtilis str. 168
5S ribosomal RNA	B	RNA	112	Bacillus subtilis subsp. subtilis str. 168
50S ribosomal protein L2	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

>7QV2_1 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN

Sequence of entity 2 (1), FASTA

>7QV2_2 50S ribosomal protein L33 1 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK

Sequence of entity 3 (2), FASTA

>7QV2_3 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA

Sequence of entity 4 (3), FASTA

>7QV2_4 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK

Sequence of entity 5 (4), FASTA

>7QV2_5 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG

Sequence of entity 6 (6), FASTA

>7QV2_6 50S ribosomal protein L31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYGLK

Sequence of entity 7 (A), FASTA

>7QV2_7 mRNA (chains A)
AAGGAAAUAAAAUGGGACGACGUAGCAUU

Sequence of entity 8 (B), FASTA

>7QV2_8 5S ribosomal RNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA

Sequence of entity 9 (C), FASTA

>7QV2_9 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 10 (D), FASTA

>7QV2_10 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 11 (E), FASTA

>7QV2_11 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 12 (F), FASTA

>7QV2_12 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Primary citation

Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Cerullo, F., Filbeck, S., Patil, P.R. et al. Nature (2022) 603:509-514. DOI 10.1038/s41586-022-04487-6 · 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
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)
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…

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