6TPQ: RNase M5
RNase M5 bound to 50S ribosome with precursor 5S rRNA. Determined by electron microscopy at 3.07 Å resolution. Released 30 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.07 Å
- Organisms
- Geobacillus stearothermophilus, Bacillus subtilis subsp. subtilis str. 168
- Chains
- 31
- Atoms
- 91,728
- Mol. weight
- 1390.81 kDa
- Ligands
- MG, ZN
- Released
- 30 Sept 2020
Explore 6TPQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6TPQ contains 119 α-helices and 193 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: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 7-10 | 4 | |
| β-strand | 18 | 1 | 25 |
| α-helix | 21-23 | 3 | |
| β-strand | 26-29 | 4 | 25 |
| β-strand | 32-35 | 4 | 25 |
| β-strand | 45-47 | 3 | 26 |
| β-strand | 50-52 | 3 | 26 |
| α-helix | 60-82 | 23 | |
| β-strand | 84-90 | 7 | 27 |
| β-strand | 96-100 | 5 | 28 |
| β-strand | 103-107 | 5 | 28 |
| β-strand | 114-116 | 3 | 28 |
| β-strand | 122-128 | 7 | 27 |
| β-strand | 131-136 | 6 | 27 |
| α-helix | 139-150 | 12 | |
| β-strand | 163-165 | 3 | 27 |
Chain A: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 123-128 | 6 | |
| α-helix | 136-147 | 12 | |
| α-helix | 155-165 | 11 | |
| α-helix | 169-183 | 15 | |
Chain b: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| β-strand | 23-24 | 2 | 5 |
| β-strand | 27 | 1 | 6 |
| α-helix | 34-47 | 14 | |
| α-helix | 61-66 | 6 | |
| α-helix | 74-76 | 3 | |
| β-strand | 83 | 1 | 6 |
| β-strand | 86-87 | 2 | 5 |
| α-helix | 95-103 | 9 | |
Chain B: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 1 |
| α-helix | 12-19 | 8 | |
| β-strand | 26-28 | 3 | 1 |
| α-helix | 36-48 | 13 | |
| β-strand | 51-53 | 3 | 1 |
| α-helix | 59-71 | 13 | |
| β-strand | 76-77 | 2 | 1 |
| α-helix | 95-97 | 3 | |
| α-helix | 100-108 | 9 | |
| β-strand | 111 | 1 | 1 |
| α-helix | 123-128 | 6 | |
| α-helix | 136-147 | 12 | |
| α-helix | 155-164 | 10 | |
| α-helix | 170-184 | 15 | |
Chain c: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 29 |
| β-strand | 25 | 1 | 30 |
| α-helix | 30-37 | 8 | |
| β-strand | 55-58 | 4 | 29 |
| α-helix | 60-62 | 3 | |
| β-strand | 64 | 1 | 30 |
| β-strand | 74-78 | 5 | 31 |
| β-strand | 85-89 | 5 | 31 |
| α-helix | 90-96 | 7 | |
| α-helix | 98-107 | 10 | |
| α-helix | 114-119 | 6 | |
| α-helix | 120-122 | 3 | |
| β-strand | 123-125 | 3 | 29 |
| β-strand | 139-140 | 2 | 29 |
Chain d: 1 helix, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 32 |
| β-strand | 7-10 | 4 | 33 |
| β-strand | 12 | 1 | 34 |
| β-strand | 16-24 | 9 | 33 |
| β-strand | 32-33 | 2 | 32 |
| β-strand | 38-46 | 9 | 33 |
| β-strand | 57-64 | 8 | 33 |
| β-strand | 70 | 1 | 35 |
| β-strand | 76-78 | 3 | 35 |
| β-strand | 83-87 | 5 | 33 |
| β-strand | 93 | 1 | 33 |
| β-strand | 98 | 1 | 34 |
| β-strand | 102 | 1 | 36 |
| α-helix | 112-117 | 6 | |
| β-strand | 121 | 1 | 36 |
Chain e: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 8-9 | 2 | |
| α-helix | 55-56 | 2 | |
| α-helix | 58-60 | 3 | |
| β-strand | 75-77 | 3 | 37 |
| α-helix | 79-83 | 5 | |
| β-strand | 91 | 1 | 38 |
| α-helix | 95-99 | 5 | |
| β-strand | 109-111 | 3 | 37 |
| β-strand | 123-125 | 3 | 38 |
| β-strand | 127-128 | 2 | 37 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-145 | 3 | 38 |
Chain f: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-35 | 4 | 39 |
| β-strand | 40-43 | 4 | 40 |
| α-helix | 44-57 | 14 | |
| β-strand | 63-66 | 4 | 39 |
| β-strand | 72-76 | 5 | 40 |
| α-helix | 77-78 | 2 | |
| β-strand | 89-97 | 9 | 40 |
| β-strand | 102-107 | 6 | 39 |
| α-helix | 111-122 | 12 | |
| β-strand | 131-133 | 3 | 39 |
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 |
|---|
| Ribonuclease M5 | A, B | protein | 187 | Geobacillus stearothermophilus | A0A087LGV4 (AlphaFold model) |
| pre-5S rRNA | V | RNA | 123 | Bacillus subtilis subsp. subtilis str. 168 | |
| 50S ribosomal protein L10 | b | protein | 166 | Bacillus subtilis subsp. subtilis str. 168 | P42923 (AlphaFold model) |
| pre-23S rRNA | U | RNA | 2924 | 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 (A, B), FASTA
>6TPQ_1 Ribonuclease M5 (chains A, B)
MKIKEVIVVEGKDDTAAIRRAVDADTIETNGAAVGAEVIERIKLAKERRGVIIFTDPAFP
GEKIRRTIAEQVPGCKHAFLPREAAKARSGKGIGVEHASPDDIRQALANVYEETADWEEE
ITFAELIEAGLVGGEMARRRRQRLGEELKIGYANGRQFHKRLKVFRISRDAFYAALAQVM
REEAGDA
Sequence of entity 2 (V), FASTA
>6TPQ_2 pre-5S rRNA (chains V)
UUUGUUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAA
GCUCUUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGC
AAG
Sequence of entity 3 (b), FASTA
>6TPQ_3 50S ribosomal protein L10 (chains b)
MSSAIETKKVVVEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVEFKVYKNTMT
RRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVSTV
EEVKALAELPSREGLLSMLLSVLQAPVRNLALAAKAVAEQKEEQGA
Sequence of entity 4 (U), FASTA
>6TPQ_4 pre-23S rRNA (chains U)
UUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGGAC
GAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUGGG
GAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAGGC
AGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCCCU
GAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUGUA
GGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCCGC
CAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGUAC
GGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUACUC
CCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGG
AGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGAUG
GCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCCCGUGCAAGGUUAAGCAGAAGAU
GCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCCGA
AACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCGAA
CCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGAAC
CUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCUUG
GAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACUCC
GAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAAAG
GGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUGUG
GAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGUAA
UAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCGAA
GCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGACC
GGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGGUG
AGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUUAG
UCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUGUA
CCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAUUG
GAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGGCUGA
GCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAAGC
CUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAAUC
CUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGG
AGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGCGA
CUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACGCC
UGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAGCC
CCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAA
GUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGUGA
AAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGC
UUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUUGG
AAACCGGAGCGCCAGCUUUGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGACC
UUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGGGG
CGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAAUC
AUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGA
CGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAA
AAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGUUU
GGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUG
UUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCU
AUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUG
GACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCGGA
CGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAUUC
CGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGUGG
CGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACC
Sequence of entity 5 (W), FASTA
>6TPQ_5 50S ribosomal protein L2 (chains W)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 6 (X), FASTA
>6TPQ_6 50S ribosomal protein L3 (chains X)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 7 (Y), FASTA
>6TPQ_7 50S ribosomal protein L4 (chains Y)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 8 (Z), FASTA
>6TPQ_8 50S ribosomal protein L5 (chains Z)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK
Sequence of entity 9 (a), FASTA
>6TPQ_9 50S ribosomal protein L6 (chains a)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK
Sequence of entity 10 (c), FASTA
>6TPQ_10 50S ribosomal protein L13 (chains c)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Sequence of entity 11 (d), FASTA
>6TPQ_11 50S ribosomal protein L14 (chains d)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI
Sequence of entity 12 (e), FASTA
>6TPQ_12 50S ribosomal protein L15 (chains e)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 219 |
| 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 A0A087LGV4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6TG6 1.3 Å, Toprim domain of RNase M5
- 6TGJ 1.5 Å, RNA-binding domain of RNase M5
- 6Z2B 2.14 Å, Toprim domain of RNase M5 bound with two Mg2+ ions
Browse structure collections
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