8CDV: Rnase R
Rnase R bound to a 30S degradation intermediate (state II). Determined by electron microscopy at 4.73 Å resolution. Released 20 Dec 2023.
- Method
- Electron microscopy
- Resolution
- 4.73 Å
- Organism
- Bacillus subtilis subsp. subtilis str. 168
- Chains
- 19
- Atoms
- 43,593
- Mol. weight
- 809.55 kDa
- Released
- 20 Dec 2023
Explore 8CDV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8CDV contains 99 α-helices and 100 β-strands across 17 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 C: 24 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| β-strand | 22 | 1 | 1 |
| α-helix | 24-30 | 7 | |
| α-helix | 36-51 | 16 | |
| β-strand | 56-57 | 2 | 1 |
| β-strand | 63-64 | 2 | 1 |
| α-helix | 228-235 | 8 | |
| α-helix | 242-245 | 4 | |
| α-helix | 248 | 1 | |
| β-strand | 249-250 | 2 | 2 |
| β-strand | 257-260 | 4 | 2 |
| β-strand | 269-275 | 7 | 2 |
| β-strand | 281-288 | 8 | 2 |
| α-helix | 290-293 | 4 | |
| α-helix | 299-307 | 9 | |
| β-strand | 309 | 1 | 3 |
| β-strand | 311-312 | 2 | 4 |
| β-strand | 317-318 | 2 | 4 |
| α-helix | 323-324 | 2 | |
| α-helix | 325-329 | 5 | |
| β-strand | 337-347 | 11 | 2 |
| β-strand | 353-364 | 12 | 2 |
| β-strand | 367-370 | 4 | 2 |
| α-helix | 371-378 | 8 | |
| α-helix | 383-388 | 6 | |
| α-helix | 393-412 | 20 | |
| β-strand | 422-427 | 6 | 5 |
| β-strand | 433-439 | 7 | 5 |
| α-helix | 443-466 | 24 | |
| β-strand | 472-474 | 3 | 6 |
| β-strand | 475 | 1 | 7 |
| α-helix | 476-479 | 4 | |
| α-helix | 480-492 | 13 | |
| α-helix | 501-503 | 3 | |
| α-helix | 506-516 | 11 | |
| α-helix | 522-532 | 11 | |
| α-helix | 534-536 | 3 | |
| β-strand | 537-539 | 3 | 6 |
| β-strand | 545 | 1 | 7 |
| α-helix | 546-548 | 3 | |
| β-strand | 550 | 1 | 7 |
| β-strand | 562 | 1 | 3 |
| α-helix | 563-572 | 10 | |
| α-helix | 573-577 | 5 | |
| α-helix | 583-615 | 33 | |
Chain F: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-15 | 8 | |
| α-helix | 47-61 | 15 | |
| α-helix | 65-77 | 13 | |
| α-helix | 82-91 | 10 | |
| β-strand | 93 | 1 | 8 |
| α-helix | 94-100 | 7 | |
| α-helix | 107-115 | 9 | |
| β-strand | 119-121 | 3 | 9 |
| β-strand | 124-125 | 2 | 9 |
| β-strand | 132 | 1 | 8 |
| β-strand | 138-141 | 4 | 9 |
| α-helix | 143-145 | 3 | |
| α-helix | 149-153 | 5 | |
| β-strand | 165-166 | 2 | 9 |
| β-strand | 173-176 | 4 | 9 |
| α-helix | 191-199 | 9 | |
Chain G: 6 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| β-strand | 12-25 | 14 | 10 |
| β-strand | 28-40 | 13 | 10 |
| β-strand | 45-53 | 9 | 10 |
| α-helix | 56-69 | 14 | |
| β-strand | 72-73 | 2 | 10 |
| β-strand | 77 | 1 | 11 |
| β-strand | 80 | 1 | 11 |
| β-strand | 85-89 | 5 | 12 |
| β-strand | 92-98 | 7 | 12 |
| β-strand | 105-106 | 2 | 12 |
| α-helix | 109-118 | 10 | |
| β-strand | 123-127 | 5 | 12 |
| α-helix | 133-144 | 12 | |
| α-helix | 147-149 | 3 | |
| α-helix | 150-157 | 8 | |
Chain H: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-30 | 10 | |
| α-helix | 36-54 | 19 | |
| α-helix | 58-68 | 11 | |
| α-helix | 93-110 | 18 | |
| α-helix | 116-127 | 12 | |
Chain I: 6 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| β-strand | 24-28 | 5 | 13 |
| α-helix | 31-42 | 12 | |
| β-strand | 46-52 | 7 | 13 |
| β-strand | 59-64 | 6 | 13 |
| β-strand | 66 | 1 | 14 |
| β-strand | 72 | 1 | 14 |
| β-strand | 77-79 | 3 | 15 |
| β-strand | 82 | 1 | 16 |
| β-strand | 85 | 1 | 16 |
| β-strand | 88-89 | 2 | 15 |
| α-helix | 91-93 | 3 | |
| α-helix | 94-96 | 3 | |
| β-strand | 97 | 1 | 17 |
| α-helix | 98-100 | 3 | |
| β-strand | 102 | 1 | 17 |
| β-strand | 103-107 | 5 | 15 |
| β-strand | 112-114 | 3 | 15 |
| α-helix | 115-120 | 6 | |
| β-strand | 125-131 | 7 | 15 |
Chain J: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-12 | 7 | 18 |
| β-strand | 15-23 | 9 | 18 |
| β-strand | 28-30 | 3 | 18 |
| β-strand | 34 | 1 | 18 |
| α-helix | 35-38 | 4 | |
| α-helix | 42-54 | 13 | |
| β-strand | 58 | 1 | 18 |
| β-strand | 61-68 | 8 | 18 |
| α-helix | 72-90 | 19 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-100 | 6 | |
Chain K: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-12 | 6 | 19 |
| α-helix | 15-31 | 17 | |
| β-strand | 35 | 1 | 20 |
| β-strand | 71-75 | 5 | 19 |
| β-strand | 77 | 1 | 20 |
| α-helix | 81-88 | 8 | |
| β-strand | 96-99 | 4 | 19 |
Chain L: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 14-16 | 3 | |
| α-helix | 22-25 | 4 | |
| β-strand | 26-29 | 4 | 21 |
| β-strand | 34-37 | 4 | 21 |
| β-strand | 42-53 | 12 | 22 |
| α-helix | 54-56 | 3 | |
| β-strand | 63-70 | 8 | 22 |
| β-strand | 75-79 | 5 | 22 |
| β-strand | 92-97 | 6 | 22 |
| β-strand | 108-110 | 3 | 22 |
| α-helix | 118-120 | 3 | |
| α-helix | 127-130 | 4 | |
9 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 |
|---|
| 16S rRNA | A | RNA | 1554 | Bacillus subtilis subsp. subtilis str. 168 | |
| RNA Substrate | B | RNA | 11 | Bacillus subtilis subsp. subtilis str. 168 | |
| Ribonuclease R | C | protein | 779 | Bacillus subtilis subsp. subtilis str. 168 | O32231 (AlphaFold model) |
| 30S ribosomal protein S4 | F | protein | 200 | Bacillus subtilis subsp. subtilis str. 168 | P21466 (AlphaFold model) |
| 30S ribosomal protein S5 | G | protein | 166 | Bacillus subtilis subsp. subtilis str. 168 | P21467 (AlphaFold model) |
| 30S ribosomal protein S7 | H | protein | 156 | Bacillus subtilis subsp. subtilis str. 168 | P21469 (AlphaFold model) |
| 30S ribosomal protein S8 | I | protein | 132 | Bacillus subtilis subsp. subtilis str. 168 | P12879 |
| 30S ribosomal protein S9 | J | protein | 130 | Bacillus subtilis subsp. subtilis str. 168 | P21470 |
| 30S ribosomal protein S10 | K | protein | 102 | Bacillus subtilis subsp. subtilis str. 168 | P21471 |
| 30S ribosomal protein S12 | L | protein | 138 | Bacillus subtilis subsp. subtilis str. 168 | P21472 |
| 30S ribosomal protein S13 | M | protein | 121 | Bacillus subtilis subsp. subtilis str. 168 | P20282 |
| 30S ribosomal protein S15 | O | protein | 89 | Bacillus subtilis subsp. subtilis str. 168 | P21473 |
7 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8CDV_1 16S rRNA (chains A)
UUUAUCGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCA
AGUCGAGCGGACAGAUGGGAGCUUGCUCCCUGAUGUUAGCGGCGGACGGGUGAGUAACAC
GUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGG
UUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGAC
CCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUGCGUAGCCGA
CCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCA
GCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUG
AAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUGCCGUUCGAAUAGGGC
GGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUA
AUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUC
UUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACU
UGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGA
GGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGU
GGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUG
UUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGU
ACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUG
UGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCU
AGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUC
GUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAG
CAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGAC
GUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAA
GGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAG
UCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGU
GAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCG
AAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUG
AAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCUA
Sequence of entity 2 (B), FASTA
>8CDV_2 RNA Substrate (chains B)
AAAAAAAAAAA
Sequence of entity 3 (C), FASTA
>8CDV_3 Ribonuclease R (chains C)
MEKEAFMEKLLSFMKEEAYKPLTVQELEEMLNITEAEEFKELVKALVALEEKGLIVRTRS
DRYGIPEKMNLIKGKISAHAKGFAFLLPEDTSLSDVFIPPNELNTAMNGDIVMVRLNSQS
SGSRQEGTVIRILERAIQRVVGTYTETRNFGFVIPDDKKITSDIFIPKNGKNGAAEGHKV
VVKLTSYPEGRMNAEGEVETILGHKNDPGIDILSVIHKHGLPGEFPADAMEQASSTPDTI
DEKDLKDRRDLRDQVIVTIDGADAKDLDDAVTVTKLDDGSYKLGVHIADVSHYVTENSPI
DKEALERGTSVYLVDRVIPMIPHRLSNGICSLNPKVDRLTLSCEMTINSQGQVTEHEIFQ
SVIKTTERMTYSDVNKILVDDDEELKQKYEPLVPMFKDMERLAQILRDKRMDRGAVDFDF
KEAKVLVDDEGAVKDVVIRERSVAEKLIEEFMLVANETVAEHFHWMNVPFIYRIHEEPNA
EKLQKFLEFVTTFGYVVKGTAGNIHPRALQSILDAVRDRPEETVISTVMLRSMKQAKYDP
QSLGHFGLSTEFYTHFTSPIRRYPDLIVHRLIRTYLINGKVDEATQEKWAERLPDIAEHT
SSMERRAVDAERETDDLKKAEYMLDKIGEEFDGMISSVTNFGMFVELPNTIEGLVHVSFM
TDDYYRFDEQHFAMIGERTGNVFRIGDEITVKVVDVNKDERNIDFEIVGMKGTPRRPREL
DSSRSRKRGKPARKRVQSTNTPVSPAPSEEKGEWFTKPKKKKKKRGFQNAPKQKRKKKK
Sequence of entity 4 (F), FASTA
>8CDV_4 30S ribosomal protein S4 (chains F)
MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHM
YGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHIL
VDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLP
ERSELAPEINEALIVEFYSR
Sequence of entity 5 (G), FASTA
>8CDV_5 30S ribosomal protein S5 (chains G)
MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAI
RKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGV
ADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG
Sequence of entity 6 (H), FASTA
>8CDV_6 30S ribosomal protein S7 (chains H)
MPRKGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKSQTILYKSFDIIKERTGNDAME
VFEQALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERL
ANEILDAANNTGAAVKKREDTHKMAEANKAFAHYRW
Sequence of entity 7 (I), FASTA
>8CDV_7 30S ribosomal protein S8 (chains I)
MVMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGII
RVFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARA
KQAGGEVLAYVW
Sequence of entity 8 (J), FASTA
>8CDV_8 30S ribosomal protein S9 (chains J)
MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGT
YDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKG
ARRAPQFSKR
Sequence of entity 9 (K), FASTA
>8CDV_9 30S ribosomal protein S10 (chains K)
MAKQKIRIRLKAYDHRILDQSAEKIVETAKRSGASVSGPIPLPTEKSVYTILRAVHKYKD
SREQFEMRTHKRLIDIVNPTPQTVDALMRLDLPSGVDIEIKL
Sequence of entity 10 (L), FASTA
>8CDV_10 30S ribosomal protein S12 (chains L)
MPTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNS
ALRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGV
ENRAQGRSKYGTKKPKAK
Sequence of entity 11 (M), FASTA
>8CDV_11 30S ribosomal protein S13 (chains M)
MARIAGVDIPRDKRVVISLTYIFGIGRTTAQQVLKEAGVSEDTRVRDLTEEELGKIRDII
DKLKVEGDLRREVSLNIKRLIEIGSYRGIRHRRGLPVRGQNSKNNARTRKGPRRTVANKK
K
Sequence of entity 12 (O), FASTA
>8CDV_12 30S ribosomal protein S15 (chains O)
MAITQERKNQLINEFKTHESDTGSPEVQIAILTDSINNLNEHLRTHKKDHHSRRGLLKMV
GKRRNLLTYLRNKDVTRYRELINKLGLRR
Primary citation
Structural basis of ribosomal 30S subunit degradation by RNase R. Dimitrova-Paternoga, L., Kasvandik, S., Beckert, B. et al. Nature (2024) 626:1133-1140. DOI 10.1038/s41586-024-07027-6 · PubMed
Other PDB entries of the same protein (UniProt O32231 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8CDU 3.1 Å, Rnase R bound to a 30S degradation intermediate (main state)
- 8CEC 3.57 Å, Rnase R bound to a 30S degradation intermediate (State I - head-turning)
- 8CEE 3.7 Å, Rnase R bound to a 30S degradation intermediate (State I - head-turning)
- 8CED 4.15 Å, Rnase R bound to a 30S degradation intermediate (State I - head-turning)
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