7QGU: B. subtilis disome - stalled 70S ribosome

Name: PDB 7QGU: Structure of the B. subtilis disome - stalled 70S ribosome
Published: 2022-03-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the B. subtilis disome - stalled 70S ribosome. Determined by electron microscopy at 4.75 Å resolution. Released 16 Mar 2022.

Method: Electron microscopy
Resolution: 4.75 Å
Organism: Bacillus subtilis
Chains: 54
Atoms: 135,606
Mol. weight: 2195.51 kDa
Released: 16 Mar 2022

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

Secondary structure: helices and β-sheets

7QGU contains 250 α-helices and 312 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 a: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	112
α-helix	17-26	10
β-strand	34-38	5	112
α-helix	41-49	9
β-strand	54-57	4	112

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-17	8
α-helix	22-26	5
β-strand	28	1	1
β-strand	37	1	1
β-strand	42	1	69
β-strand	48-49	2	2
β-strand	52-53	2	2

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	3
β-strand	17-20	4	3
α-helix	29-30	2
β-strand	31-36	6	3
β-strand	41-47	7	3

Chain C: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	4
α-helix	6-7	2
β-strand	17-19	3	4
α-helix	31-33	3
β-strand	34-35	2	5
β-strand	43	1	6
β-strand	49	1	6
β-strand	62-63	2	5
α-helix	64	1
β-strand	65	1	7
β-strand	75-82	8	7
α-helix	90	1
β-strand	91-96	6	7
β-strand	101-105	5	7
β-strand	107	1	8
β-strand	115-117	3	7
β-strand	129-131	3	9
α-helix	132-134	3
α-helix	136	1
β-strand	140	1	10
β-strand	141-142	2	9
β-strand	163	1	10
β-strand	172-175	4	10
α-helix	177-179	3
β-strand	181-184	4	10
β-strand	189-192	4	9
β-strand	195	1	8
α-helix	198-202	5
α-helix	208-214	7
α-helix	265-269	5
β-strand	270-272	3	10

Chain d: 3 helices, 0 β-strands

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

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
β-strand	12-14	3	12
β-strand	17	1	13
β-strand	19	1	13
β-strand	24-28	5	12
β-strand	33-34	2	14
β-strand	35-38	4	15
β-strand	49-52	4	15
β-strand	55	1	16
α-helix	58-60	3
α-helix	63-68	6
β-strand	77	1	16
β-strand	80-81	2	15
β-strand	96-97	2	14
β-strand	107-113	7	12
α-helix	114-116	3
β-strand	118-120	3	17
α-helix	122-126	5
α-helix	128-132	5
α-helix	154-155	2
β-strand	162-164	3	17
β-strand	168-180	13	12
β-strand	185-189	5	12
β-strand	201	1	12
β-strand	203	1	11
β-strand	204	1	12
α-helix	205-206	2

Chain e: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-13	6
β-strand	15-16	2	18
β-strand	22-25	4	18
α-helix	26	1
α-helix	38-45	8
β-strand	47-49	3	18
α-helix	50-51	2
α-helix	52-58	7

Chain E: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	19
α-helix	27-28	2
α-helix	30-41	12
α-helix	100-102	3
α-helix	103-119	17
β-strand	123-126	4	19
α-helix	137-145	9
β-strand	152-155	4	19
α-helix	161-165	5
β-strand	173-176	4	19
α-helix	178-180	3
α-helix	183-188	6
β-strand	192-194	3	19
α-helix	196-205	10

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
23S rRNA	A	RNA	2928	Bacillus subtilis
5S rRNA	B	RNA	119	Bacillus subtilis
50S ribosomal protein L2	C	protein	277	Bacillus subtilis	P42919 (AlphaFold model)
50S ribosomal protein L3	D	protein	208	Bacillus subtilis	P42920 (AlphaFold model)
50S ribosomal protein L4	E	protein	207	Bacillus subtilis	P42921 (AlphaFold model)
50S ribosomal protein L5	F	protein	179	Bacillus subtilis	P12877 (AlphaFold model)
Ribosomal protein L6	G	protein	179	Bacillus subtilis	P46898
50S ribosomal protein L10	H	protein	166	Bacillus subtilis	P42923
50S ribosomal protein L11	I	protein	141	Bacillus subtilis	Q06796
50S ribosomal protein L13	J	protein	145	Bacillus subtilis	P70974
50S ribosomal protein L14	K	protein	122	Bacillus subtilis	P12875
50S ribosomal protein L15	L	protein	146	Bacillus subtilis	P19946

42 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7QGU_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
UGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGCCU
GAGCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAA
GCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAA
UCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCG
GGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGC
GACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACG
CCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAG
CCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGU
AAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGU
GAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGA
GCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUU
GGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGA
CCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGG
GGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAA
UCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGG
GACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAU
AAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGU
UUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGC
UGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCC
CUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGA
UGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCG
GACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAU
UCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGU
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCAU

Sequence of entity 2 (B), FASTA

>7QGU_2 5S rRNA (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG

Sequence of entity 3 (C), FASTA

>7QGU_3 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 4 (D), FASTA

>7QGU_4 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKS

Sequence of entity 5 (E), FASTA

>7QGU_5 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 6 (F), FASTA

>7QGU_6 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Sequence of entity 7 (G), FASTA

>7QGU_7 Ribosomal protein L6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK

Sequence of entity 8 (H), FASTA

>7QGU_8 50S ribosomal protein L10 (chains H)
MSSAIETKKVVVEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVEFKVYKNTMT
RRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVSTV
EEVKALAELPSREGLLSMLLSVLQAPVRNLALATKAVAEQKEEQGA

Sequence of entity 9 (I), FASTA

>7QGU_9 50S ribosomal protein L11 (chains I)
MAKKVVKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTADQAGLIIPVEISV
YEDRSFTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATVKRDKVREIAETKMPDLNAAD
VEAAMRMVEGTARSMGIVIED

Sequence of entity 10 (J), FASTA

>7QGU_10 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG

Sequence of entity 11 (K), FASTA

>7QGU_11 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI

Sequence of entity 12 (L), FASTA

>7QGU_12 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI

Primary citation

Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Saito, K., Kratzat, H., Campbell, A. et al. Nature (2022) 603:503-508. DOI 10.1038/s41586-022-04416-7 · 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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