6TNN: Mini-RNase III

Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA. Determined by electron microscopy at 3.07 Å resolution. Released 30 Sept 2020.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 31
Atoms: 91,840
Mol. weight: 1381.5 kDa
Ligands: MG, ZN
Released: 30 Sept 2020

Explore 6TNN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TNN contains 104 α-helices and 186 β-strands across 29 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	22
β-strand	26-29	4	22
β-strand	32-35	4	22
β-strand	43-47	5	23
β-strand	50-54	5	23
α-helix	62-81	20
β-strand	84-89	6	24
β-strand	90	1	25
β-strand	96-100	5	26
β-strand	103-107	5	26
α-helix	113	1
β-strand	114-116	3	26
β-strand	122-128	7	24
β-strand	131-136	6	24
α-helix	139-150	12
α-helix	154-156	3
β-strand	163	1	25

Chain b: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
β-strand	24	1	1
α-helix	34-47	14
α-helix	60-66	7
β-strand	86	1	1
α-helix	94-103	10

Chain c: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	27
β-strand	25	1	28
α-helix	33-36	4
β-strand	55-58	4	27
α-helix	60-62	3
β-strand	64	1	28
α-helix	69-72	4
β-strand	74-78	5	29
β-strand	85-89	5	29
α-helix	90-96	7
α-helix	98-107	10
α-helix	119-122	4
β-strand	123-125	3	27
β-strand	139-140	2	27

Chain d: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	30
β-strand	7-10	4	31
β-strand	16-24	9	31
β-strand	33	1	30
β-strand	38-46	9	31
β-strand	57-64	8	31
β-strand	69-70	2	32
β-strand	76-78	3	32
β-strand	83-87	5	31
β-strand	93	1	31
α-helix	112-115	4

Chain e: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
α-helix	55-56	2
α-helix	57-60	4
β-strand	77	1	33
α-helix	79-83	5
α-helix	86	1
β-strand	91	1	34
α-helix	95-99	5
β-strand	110-111	2	33
β-strand	123	1	34
β-strand	124	1	35
β-strand	127-128	2	33
α-helix	132-138	7
β-strand	144	1	35

Chain f: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	32-36	5	36
β-strand	40-42	3	37
α-helix	44-57	14
β-strand	63-64	2	36
β-strand	72-76	5	38
α-helix	77-78	2
β-strand	89-94	6	38
β-strand	95-97	3	37
β-strand	102	1	36
β-strand	106-107	2	36
α-helix	111-122	12
β-strand	129-133	5	36
α-helix	134-135	2

Chain g: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
β-strand	29-33	5	39
α-helix	35-38	4
α-helix	44-51	8
α-helix	56-63	8
α-helix	79-89	11
β-strand	100-106	7	39
β-strand	113-118	6	39

Chain h: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-19	13
β-strand	25	1	40
β-strand	28	1	40
β-strand	30-35	6	41
β-strand	40-45	6	41
β-strand	52-57	6	41
α-helix	71-88	18
β-strand	94-95	2	41
α-helix	104-115	12

21 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 L10	b	protein	166	Bacillus subtilis subsp. subtilis str. 168	P42923 (AlphaFold model)
Mini-ribonuclease 3	H, I	protein	143	Bacillus subtilis subsp. subtilis str. 168	O31418 (AlphaFold model)
pre-23S rRNA	U	RNA	2930	Bacillus subtilis subsp. subtilis str. 168
5S rRNA	V	RNA	116	Bacillus subtilis subsp. subtilis str. 168
50S ribosomal protein L2	W	protein	277	Bacillus subtilis subsp. subtilis str. 168	P42919 (AlphaFold model)
50S ribosomal protein L3	X	protein	209	Bacillus subtilis subsp. subtilis str. 168	P42920 (AlphaFold model)
50S ribosomal protein L4	Y	protein	207	Bacillus subtilis subsp. subtilis str. 168	P42921
50S ribosomal protein L5	Z	protein	179	Bacillus subtilis subsp. subtilis str. 168	P12877
50S ribosomal protein L6	a	protein	179	Bacillus subtilis subsp. subtilis str. 168	P46898
50S ribosomal protein L13	c	protein	145	Bacillus subtilis subsp. subtilis str. 168	P70974
50S ribosomal protein L14	d	protein	122	Bacillus subtilis subsp. subtilis str. 168	P12875
50S ribosomal protein L15	e	protein	146	Bacillus subtilis subsp. subtilis str. 168	P19946

18 more molecules are not listed.

Sequence of entity 1 (b), FASTA

>6TNN_1 50S ribosomal protein L10 (chains b)
MSSAIETKKVVVEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVEFKVYKNTMT
RRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVSTV
EEVKALAELPSREGLLSMLLSVLQAPVRNLALAAKAVAEQKEEQGA

Sequence of entity 2 (H, I), FASTA

>6TNN_2 Mini-ribonuclease 3 (chains H, I)
MLEFDTIKDSKQLNGLALAYIGNAIFEVYVRHHLLKQGFTKPNDLHKKSSRIVSAKSQAE
ILFFLQNQSFFTEEEEAVLKRGRNAKSGTTPKNTDVQTYRYSTAFEALLGYLFLEKKEER
LSQLVAEAIQFGTSGRKTNESAT

Sequence of entity 3 (U), FASTA

>6TNN_3 pre-23S rRNA (chains U)
ACGGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACG
GGACGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAA
UGGGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGA
AGGCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUU
CCCUGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGU
UGUAGGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGC
CCGCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGA
GUACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAU
ACUCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAA
GGGGAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGU
GAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCCCGUGCAAGGUUAAGCAGA
AGAUGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGAC
CCGAAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCC
CGAACCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUC
GAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGU
CUUGGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAA
CUCCGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCG
AAAGGGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGA
UGUGGAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGC
GUAAUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCAC
CGAAGCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCA
GACCGGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGG
GGUGAGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGG
UUAGUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCC
UGUACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGU
AUUGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGG
CUGAGCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAA
AAGCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAG
AAUCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUU
CGGGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAG
GCGACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGA
CGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGA
AGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGG
GUAAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCG
GUGAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUG
GAGCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCC
UUGGAAACCGGAGCGCCAGCUUUGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUU
GACCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACU
GGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGA
AAUCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCA
GGGACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGG
AUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAG
GUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGG
GCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGU
CCCUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGG
GAUGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUG
CGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCC
AUUCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGU
GUGGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCAU

Sequence of entity 4 (V), FASTA

>6TNN_4 5S rRNA (chains V)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGC

Sequence of entity 5 (W), FASTA

>6TNN_5 50S ribosomal protein L2 (chains W)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK

Sequence of entity 6 (X), FASTA

>6TNN_6 50S ribosomal protein L3 (chains X)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK

Sequence of entity 7 (Y), FASTA

>6TNN_7 50S ribosomal protein L4 (chains Y)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA

Sequence of entity 8 (Z), FASTA

>6TNN_8 50S ribosomal protein L5 (chains Z)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK

Sequence of entity 9 (a), FASTA

>6TNN_9 50S ribosomal protein L6 (chains a)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK

Sequence of entity 10 (c), FASTA

>6TNN_10 50S ribosomal protein L13 (chains c)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG

Sequence of entity 11 (d), FASTA

>6TNN_11 50S ribosomal protein L14 (chains d)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI

Sequence of entity 12 (e), FASTA

>6TNN_12 50S ribosomal protein L15 (chains e)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	221
ZN	Zinc ion	Zn	3

Primary citation

Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs. Oerum, S., Dendooven, T., Catala, M. et al. Mol Cell (2020) 80:227. DOI 10.1016/j.molcel.2020.09.008 · PubMed

Other PDB entries of the same protein (UniProt P42923 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AS8 2.9 Å, Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with…
6TPQ 3.07 Å, RNase M5 bound to 50S ribosome with precursor 5S rRNA
7OPE 3.2 Å, RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)
7O5B 3.33 Å, Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex…
7AS9 3.5 Å, Bacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S…
5NJT 3.8 Å, Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S…
3J9W 3.9 Å, Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex
7QGU 4.75 Å, Structure of the B. subtilis disome - stalled 70S ribosome
7QH4 5.45 Å, Structure of the B. subtilis disome - collided 70S ribosome

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