7OPE: RqcH DR variant

Name: PDB 7OPE: RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)
Published: 2021-07-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement). Determined by electron microscopy at 3.2 Å resolution. Released 21 Jul 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 33
Atoms: 93,862
Mol. weight: 1460.82 kDa
Released: 21 Jul 2021

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

Secondary structure: helices and β-sheets

7OPE contains 131 α-helices and 241 β-strands across 30 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: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
β-strand	22	1	31
β-strand	23-31	9	32
β-strand	34-41	8	32
β-strand	44-51	8	32
β-strand	58-60	3	32
α-helix	74-83	10
β-strand	87-92	6	31
β-strand	99-107	9	31
β-strand	113-121	9	31
β-strand	128-133	6	31
β-strand	138	1	33
β-strand	139-142	4	31
α-helix	148-150	3
β-strand	161	1	33
α-helix	162	1
α-helix	180-184	5
α-helix	187-189	3
α-helix	192-195	4
α-helix	205-212	8
α-helix	224-235	12
β-strand	242-245	4	34
β-strand	250-253	4	34
β-strand	263-266	4	34
α-helix	270-276	7
α-helix	284-316	33
α-helix	322-334	13
β-strand	345-349	5	35
β-strand	358-362	5	35
α-helix	369-412	44
α-helix	416-428	13
β-strand	451-454	4	36
α-helix	456-458	3
β-strand	460-464	5	36
α-helix	467-476	10
β-strand	483-487	5	36
β-strand	492	1	37
β-strand	494-497	4	36
α-helix	504-516	13
β-strand	518	1	37
β-strand	526-532	7	36
α-helix	533-535	3
β-strand	536	1	38
β-strand	549	1	38
β-strand	552-557	6	36
α-helix	562-564	3

Chain 1: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	24
α-helix	3-9	7
α-helix	16-25	10
β-strand	29-30	2	25
β-strand	33-34	2	25
β-strand	40	1	24
β-strand	46-51	6	25
β-strand	54-60	7	25
α-helix	71-75	5
β-strand	76-82	7	25

Chain a: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	30-31	2	75
β-strand	38-39	2	76
β-strand	44-47	4	75
β-strand	53-54	2	76
β-strand	59-61	3	75
β-strand	67-69	3	75
β-strand	73-79	7	76
β-strand	85-90	6	76

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	77
α-helix	20-22	3
β-strand	24-29	6	77
β-strand	33-36	4	78
β-strand	39	1	79
β-strand	44	1	79
β-strand	47-50	4	78
α-helix	51-54	4

Chain c: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-7	6
α-helix	13-34	22
α-helix	41-64	24

Chain d: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	80
α-helix	17-26	10
β-strand	35-38	4	80
α-helix	41-50	10
β-strand	54-58	5	80

Chain E: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	5
β-strand	17-19	3	5
β-strand	34-35	2	6
β-strand	43	1	7
β-strand	49	1	7
β-strand	54	1	8
β-strand	62-63	2	6
β-strand	76-83	8	9
β-strand	90-96	7	9
β-strand	101-105	5	9
β-strand	107	1	10
β-strand	115-116	2	9
β-strand	129-131	3	11
β-strand	140-142	3	11
β-strand	162-163	2	11
β-strand	164-167	4	12
β-strand	171-176	6	12
β-strand	180-185	6	12
β-strand	189-192	4	11
β-strand	195	1	10
α-helix	208-213	6
β-strand	216	1	8
α-helix	217-218	2
β-strand	247	1	13
β-strand	253	1	13
β-strand	270	1	12

Chain f: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	23-25	3
β-strand	27-29	3	1
β-strand	36-38	3	1
β-strand	41	1	56
β-strand	43	1	2
β-strand	48-49	2	2
β-strand	52-53	2	2

22 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
23S rRNA	A	RNA	2926	Bacillus subtilis subsp. subtilis str. 168
5S rRNA	B	RNA	119	Bacillus subtilis subsp. subtilis str. 168
50S ribosomal protein L2	E	protein	277	Bacillus subtilis subsp. subtilis str. 168	P42919 (AlphaFold model)
50S ribosomal protein L3	F	protein	209	Bacillus subtilis subsp. subtilis str. 168	P42920 (AlphaFold model)
50S ribosomal protein L4	G	protein	207	Bacillus subtilis subsp. subtilis str. 168	P42921 (AlphaFold model)
50S ribosomal protein L5	H	protein	179	Bacillus subtilis subsp. subtilis str. 168	P12877 (AlphaFold model)
50S ribosomal protein L6	I	protein	179	Bacillus subtilis subsp. subtilis str. 168	P46898
50S ribosomal protein L11	K	protein	141	Bacillus subtilis subsp. subtilis str. 168	Q06796
50S ribosomal protein L10	L	protein	166	Bacillus subtilis subsp. subtilis str. 168	P42923
50S ribosomal protein L13	N	protein	145	Bacillus subtilis subsp. subtilis str. 168	P70974
50S ribosomal protein L14	O	protein	122	Bacillus subtilis subsp. subtilis str. 168	P12875
50S ribosomal protein L15	P	protein	146	Bacillus subtilis subsp. subtilis str. 168	P19946

21 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7OPE_1 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
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACC

Sequence of entity 2 (B), FASTA

>7OPE_2 5S rRNA (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG

Sequence of entity 3 (E), FASTA

>7OPE_3 50S ribosomal protein L2 (chains E)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 4 (F), FASTA

>7OPE_4 50S ribosomal protein L3 (chains F)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 5 (G), FASTA

>7OPE_5 50S ribosomal protein L4 (chains G)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 6 (H), FASTA

>7OPE_6 50S ribosomal protein L5 (chains H)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Sequence of entity 7 (I), FASTA

>7OPE_7 50S ribosomal protein L6 (chains I)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK

Sequence of entity 8 (K), FASTA

>7OPE_8 50S ribosomal protein L11 (chains K)
MAKKVVKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTADQAGLIIPVEISV
YEDRSFTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATVKRDKVREIAETKMPDLNAAD
VEAAMRMVEGTARSMGIVIED

Sequence of entity 9 (L), FASTA

>7OPE_9 50S ribosomal protein L10 (chains L)
MSSAIETKKVVVEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVEFKVYKNTMT
RRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVSTV
EEVKALAELPSREGLLSMLLSVLQAPVRNLALAAKAVAEQKEEQGA

Sequence of entity 10 (N), FASTA

>7OPE_10 50S ribosomal protein L13 (chains N)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG

Sequence of entity 11 (O), FASTA

>7OPE_11 50S ribosomal protein L14 (chains O)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI

Sequence of entity 12 (P), FASTA

>7OPE_12 50S ribosomal protein L15 (chains P)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI

Primary citation

RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system. Takada, H., Crowe-McAuliffe, C., Polte, C. et al. Nucleic Acids Res (2021) 49:8355-8369. DOI 10.1093/nar/gkab589 · PubMed

Other PDB entries of the same protein (UniProt P42919 (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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