8QPP: Bacillus subtilis MutS2-collided disome complex

Name: PDB 8QPP: Bacillus subtilis MutS2-collided disome complex (stalled 70S)
Published: 2023-12-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Bacillus subtilis MutS2-collided disome complex (stalled 70S). Determined by electron microscopy at 3.4 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Bacillus subtilis
Chains: 53
Atoms: 142,619
Mol. weight: 2234.26 kDa
Released: 27 Dec 2023

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

Secondary structure: helices and β-sheets

8QPP contains 214 α-helices and 304 β-strands across 48 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	21-24	4
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, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	7-9	3	4
β-strand	18-22	5	3
β-strand	32-36	5	4
β-strand	41-47	7	4

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	3-6	4
α-helix	8-11	4
β-strand	15-16	2	6
α-helix	18-20	3
β-strand	22-24	3	6
α-helix	38-45	8
β-strand	48-49	2	6
α-helix	52-58	7
α-helix	60-62	3

Chain 4: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	14
β-strand	15-19	5	14
β-strand	22-26	5	14
β-strand	34-35	2	14

Chain 6: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	19
β-strand	21-26	6	19
β-strand	30-33	4	19

Chain 9: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	99
α-helix	10-12	3
β-strand	19-20	2	99
α-helix	21-22	2
α-helix	26-30	5
α-helix	43-71	29
β-strand	79-81	3	100
β-strand	84	1	101
β-strand	90	1	101
α-helix	96-103	8
α-helix	112-114	3
α-helix	120-122	3
β-strand	127	1	100
β-strand	145-147	3	100

Chain a: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	15
β-strand	22-29	8	15
β-strand	34-39	6	16
α-helix	41-44	4
β-strand	48-52	5	16
β-strand	55	1	17
α-helix	63-70	8
α-helix	75-76	2
β-strand	77	1	17
β-strand	80-84	5	16
α-helix	88-90	3
β-strand	96	1	16
β-strand	107-113	7	15
α-helix	114-116	3
β-strand	120	1	18
α-helix	122-126	5
β-strand	162	1	18
β-strand	168-180	13	15
β-strand	185-189	5	15
β-strand	199-204	6	15

40 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	O34687 (AlphaFold model)
Large ribosomal subunit protein bL33	1	protein	48	Bacillus subtilis	P56849 (AlphaFold model)
Large ribosomal subunit protein bL34	2	protein	44	Bacillus subtilis	P05647 (AlphaFold model)
Large ribosomal subunit protein bL35	3	protein	66	Bacillus subtilis	P55874 (AlphaFold model)
50S ribosomal protein L36	4	protein	37	Bacillus subtilis	P20278
Large ribosomal subunit protein bL31	6	protein	64	Bacillus subtilis	Q03223
30S ribosomal protein S2	B	protein	246	Bacillus subtilis	P21464
30S ribosomal protein S3	C	protein	218	Bacillus subtilis	P21465
30S ribosomal protein S4	D	protein	200	Bacillus subtilis	P21466
30S ribosomal protein S5	E	protein	166	Bacillus subtilis	P21467
30S ribosomal protein S6	F	protein	95	Bacillus subtilis	P21468
30S ribosomal protein S7	G	protein	156	Bacillus subtilis	P21469

41 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8QPP_1 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN

Sequence of entity 2 (1), FASTA

>8QPP_2 Large ribosomal subunit protein bL33 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRET

Sequence of entity 3 (2), FASTA

>8QPP_3 Large ribosomal subunit protein bL34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA

Sequence of entity 4 (3), FASTA

>8QPP_4 Large ribosomal subunit protein bL35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSSVVSAGDFKRIKQ
MLANIK

Sequence of entity 5 (4), FASTA

>8QPP_5 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG

Sequence of entity 6 (6), FASTA

>8QPP_6 Large ribosomal subunit protein bL31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYG

Sequence of entity 7 (B), FASTA

>8QPP_7 30S ribosomal protein S2 (chains B)
MSVISMKQLLEAGVHFGHQTRRWNPKMKRYIFTERNGIYIIDLQKTVKKVEEAYNFTKNL
AAEGGKILFVGTKKQAQDSVKEEAQRSGMYYVNQRWLGGTLTNFETIQKRIKRLKDIEKM
QENGTFDVLPKKEVVQLKKELERLEKFLGGIKDMKDLPDALFIIDPRKERIAVAEARKLN
IPIIGIVDTNCDPDEIDVVIPANDDAIRAVKLLTSKMADAILEAKQGEEEAEVAEETAPE
TETTTA

Sequence of entity 8 (C), FASTA

>8QPP_8 30S ribosomal protein S3 (chains C)
MGQKVNPVGLRIGVIRDWESKWYAGKDYADFLHEDLKIREYISKRLSDASVSKVEIERAA
NRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIA
RQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRAD
IDYATSEADTTYGKLGVKVWIYRGEVLPTKKKTEEGGK

Sequence of entity 9 (D), FASTA

>8QPP_9 30S ribosomal protein S4 (chains D)
MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHM
YGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHIL
VDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLP
ERSELAPEINEALIVEFYSR

Sequence of entity 10 (E), FASTA

>8QPP_10 30S ribosomal protein S5 (chains E)
MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAI
RKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGV
ADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG

Sequence of entity 11 (F), FASTA

>8QPP_11 30S ribosomal protein S6 (chains F)
MRKYEVMYIIRPNIDEESKKAVIERFNNVLTSNGAEITGTKDWGKRRLAYEINDFRDGFY
QIVNVQSDAAAVQEFDRLAKISDDIIRHIVVKEEE

Sequence of entity 12 (G), FASTA

>8QPP_12 30S ribosomal protein S7 (chains G)
MPRKGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKSQTILYKSFDIIKERTGNDAME
VFEQALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERL
ANEILDAANNTGAAVKKREDTHKMAEANKAFAHYRW

Primary citation

B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage. Park, E.N., Mackens-Kiani, T., Berhane, R. et al. EMBO J (2024) 43:484-506. DOI 10.1038/s44318-023-00010-3 · 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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