7QV3: Bacillus subtilis MutS2-collided disome complex

Name: PDB 7QV3: Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)
Published: 2022-03-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S). Determined by electron microscopy at 5.14 Å resolution. Released 9 Mar 2022.

Method: Electron microscopy
Resolution: 5.14 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 55
Atoms: 149,707
Mol. weight: 2306.61 kDa
Released: 9 Mar 2022

Explore 7QV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QV3 contains 276 α-helices and 324 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-17	8
α-helix	18-20	3
β-strand	27-29	3	1
β-strand	36-38	3	1
β-strand	48-49	2	2
β-strand	52-53	2	2

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	11
β-strand	17-22	6	11
β-strand	31-36	6	11
β-strand	41-47	7	11

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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	23
α-helix	18-20	3
β-strand	22-25	4	23
α-helix	33-35	3
α-helix	38-44	7
β-strand	47-49	3	23
α-helix	52-58	7
α-helix	59-61	3

Chain 4: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	28
β-strand	15-17	3	28
α-helix	19-21	3
β-strand	24-26	3	28
α-helix	30-32	3
β-strand	34-35	2	28

Chain 6: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-15	6	29
β-strand	21-26	6	29
β-strand	30-32	3	29
α-helix	41-44	4
α-helix	48-53	6
α-helix	55-57	3

Chain b: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-22	11
α-helix	23-25	3
α-helix	31-34	4
α-helix	41-54	14

Chain c: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	39
β-strand	16	1	39
β-strand	20	1	40
α-helix	28-46	19
β-strand	53-58	6	40
β-strand	62-68	7	40
α-helix	72-74	3
α-helix	80-94	15
β-strand	97-103	7	40
α-helix	112-124	13
α-helix	131-143	13
β-strand	147-154	8	41
β-strand	165-170	6	41
β-strand	182-190	9	41
β-strand	193-202	10	41

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
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	26	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

42 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>7QV3_1 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN

Sequence of entity 2 (1), FASTA

>7QV3_2 50S ribosomal protein L33 1 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK

Sequence of entity 3 (2), FASTA

>7QV3_3 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA

Sequence of entity 4 (3), FASTA

>7QV3_4 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK

Sequence of entity 5 (4), FASTA

>7QV3_5 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG

Sequence of entity 6 (6), FASTA

>7QV3_6 50S ribosomal protein L31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYGLK

Sequence of entity 7 (A), FASTA

>7QV3_7 mRNA (chains A)
AAUAAAUGAUGCAGACAGUACUAGAU

Sequence of entity 8 (B), FASTA

>7QV3_8 5S ribosomal RNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA

Sequence of entity 9 (C), FASTA

>7QV3_9 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 10 (D), FASTA

>7QV3_10 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 11 (E), FASTA

>7QV3_11 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 12 (F), FASTA

>7QV3_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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