8QCQ: B. subtilis ApdA-stalled ribosomal complex

B. subtilis ApdA-stalled ribosomal complex. Determined by electron microscopy at 2.3 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 2.3 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Amycolatopsis japonica
Chains: 50
Atoms: 136,664
Mol. weight: 2105.87 kDa
Ligands: ZN, MG, PRO
Released: 20 Mar 2024

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

Secondary structure: helices and β-sheets

8QCQ contains 216 α-helices and 278 β-strands across 43 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
α-helix	22-25	4
β-strand	27-29	3	1
β-strand	36-38	3	1
β-strand	41	1	2
β-strand	48	1	3
β-strand	53	1	3

Chain 1: 1 helix, 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	41-47	7	7

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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	14-16	3	9
β-strand	22-24	3	9
α-helix	25-26	2
α-helix	33-35	3
α-helix	38-44	7
β-strand	48-49	2	9
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	10
β-strand	15-19	5	10
β-strand	22-26	5	10
α-helix	30-32	3
β-strand	34-36	3	10

Chain 6: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-11	2	13
β-strand	14-16	3	14
β-strand	21-22	2	14
β-strand	25-26	2	13
β-strand	31-33	3	14
α-helix	41-44	4

Chain c: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-11	5
β-strand	12	1	45
β-strand	16	1	45
β-strand	20-21	2	46
α-helix	28-45	18
β-strand	51-58	8	46
β-strand	62-69	8	46
α-helix	72-76	5
α-helix	82-94	13
β-strand	97-104	8	46
α-helix	112-124	13
α-helix	129-142	14
β-strand	147-154	8	47
β-strand	163-170	8	47
β-strand	180-190	11	47
β-strand	193-204	12	47

Chain C: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	20
α-helix	6-7	2
β-strand	17-19	3	20
α-helix	31-33	3
β-strand	34-37	4	21
β-strand	43	1	22
β-strand	49	1	22
β-strand	54	1	23
β-strand	60-63	4	21
β-strand	65	1	24
β-strand	72	1	25
β-strand	76-82	7	24
β-strand	91-96	6	24
β-strand	101-105	5	24
β-strand	107	1	26
β-strand	115-116	2	24
β-strand	118	1	25
β-strand	129-131	3	25
α-helix	132-134	3
α-helix	136	1
β-strand	140-142	3	25
β-strand	144	1	27
β-strand	154	1	27
β-strand	162-168	7	25
β-strand	171-175	5	25
β-strand	181-185	5	25
β-strand	189-192	4	25
β-strand	195	1	26
α-helix	198-202	5
α-helix	208-213	6
β-strand	216	1	23
α-helix	217-221	5
α-helix	222-224	3
β-strand	247	1	28
β-strand	253	1	28
α-helix	261	1
α-helix	265-269	5
β-strand	270-272	3	25

35 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
Large ribosomal subunit protein bL31-A	6	protein	65	Bacillus subtilis subsp. subtilis str. 168	Q03223
23S rRNA	A	RNA	2925	Bacillus subtilis subsp. subtilis str. 168
5S rRNA	B	RNA	119	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

37 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8QCQ_1 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN

Sequence of entity 2 (1), FASTA

>8QCQ_2 50S ribosomal protein L33 1 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK

Sequence of entity 3 (2), FASTA

>8QCQ_3 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA

Sequence of entity 4 (3), FASTA

>8QCQ_4 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK

Sequence of entity 5 (4), FASTA

>8QCQ_5 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG

Sequence of entity 6 (6), FASTA

>8QCQ_6 Large ribosomal subunit protein bL31-A (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRKFASADGRVDRFNK
KYGLK

Sequence of entity 7 (A), FASTA

>8QCQ_7 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
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAAC

Sequence of entity 8 (B), FASTA

>8QCQ_8 5S rRNA (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG

Sequence of entity 9 (C), FASTA

>8QCQ_9 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 10 (D), FASTA

>8QCQ_10 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 11 (E), FASTA

>8QCQ_11 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 12 (F), FASTA

>8QCQ_12 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5
MG	Magnesium ion	Mg	199
PRO	Proline	C5 H9 N O2	1

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

Primary citation

RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Morici, M., Gabrielli, S., Fujiwara, K. et al. Nat Commun (2024) 15:2432-2432. DOI 10.1038/s41467-024-46761-3 · 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
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…
7AQD 3.1 Å, Structure of the bacterial RQC complex (Translocating State)

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