8CDU: Rnase R

Rnase R bound to a 30S degradation intermediate (main state). Determined by electron microscopy at 3.1 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 22
Atoms: 51,964
Mol. weight: 868.53 kDa
Released: 20 Dec 2023

Explore 8CDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CDU contains 119 α-helices and 152 β-strands across 20 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: 30 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
β-strand	22-23	2	1
α-helix	24-27	4
α-helix	28-32	5
α-helix	36-51	16
β-strand	56-58	3	1
β-strand	62-64	3	1
α-helix	66-70	5
β-strand	75-78	4	2
β-strand	84-87	4	2
α-helix	95-96	2
β-strand	97	1	3
β-strand	98	1	2
β-strand	111	1	2
β-strand	126	1	3
β-strand	134	1	2
β-strand	139-146	8	4
β-strand	151-155	5	4
β-strand	164-166	3	4
α-helix	167	1
α-helix	168-170	3
β-strand	178-183	6	4
β-strand	189	1	5
β-strand	192	1	5
α-helix	193	1
β-strand	194-195	2	4
β-strand	201-204	4	4
α-helix	210-218	9
α-helix	225-226	2
α-helix	227-235	9
α-helix	242-245	4
β-strand	249-250	2	6
β-strand	257	1	6
β-strand	258-260	3	7
β-strand	269-275	7	6
β-strand	281-288	8	6
α-helix	290-293	4
α-helix	299-307	9
β-strand	309	1	8
β-strand	311-312	2	9
β-strand	317-318	2	9
α-helix	323-324	2
α-helix	325-329	5
β-strand	337-347	11	6
β-strand	353-364	12	6
β-strand	368-370	3	7
α-helix	371-375	5
α-helix	376-380	5
α-helix	383-388	6
α-helix	393-413	21
β-strand	423-427	5	10
β-strand	433-438	6	10
α-helix	443-466	24
β-strand	472-475	4	11
α-helix	476-479	4
α-helix	480-489	10
α-helix	506-515	10
α-helix	522-532	11
β-strand	536-539	4	11
β-strand	545	1	11
α-helix	546-548	3
β-strand	550	1	11
β-strand	562	1	8
α-helix	563-572	10
α-helix	573-577	5
α-helix	583-622	40
β-strand	627	1	12
β-strand	630-637	8	13
β-strand	644-647	4	13
β-strand	651-654	4	13
β-strand	666-668	3	14
β-strand	673-675	3	14
β-strand	682-684	3	14
β-strand	688-692	5	13
β-strand	693	1	12
β-strand	697	1	15
β-strand	702	1	15
β-strand	704	1	13
β-strand	707	1	13

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	16
α-helix	25-27	3
β-strand	31-34	4	17
β-strand	38	1	16
β-strand	39-41	3	17
α-helix	43-61	19
β-strand	67-70	4	18
α-helix	74-76	3
α-helix	77-86	10
β-strand	90-92	3	18
α-helix	104-123	20
α-helix	131-147	17
β-strand	160-164	5	18
α-helix	170-178	9
β-strand	183-186	4	18
β-strand	198-199	2	18
α-helix	207-225	19

Chain E: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	19
β-strand	16	1	19
β-strand	20-21	2	20
α-helix	28-45	18
β-strand	51-57	7	20
β-strand	64-69	6	20
α-helix	72-76	5
α-helix	81-94	14
β-strand	101	1	20
β-strand	104	1	20
α-helix	112-124	13
α-helix	129-143	15
β-strand	147-152	6	21
β-strand	165-170	6	21
β-strand	179-189	11	21
β-strand	194-205	12	21

Chain F: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	47-61	15
α-helix	65-76	12
α-helix	82-92	11
β-strand	93	1	22
α-helix	94-100	7
α-helix	107-115	9
β-strand	119-121	3	23
β-strand	124-125	2	23
β-strand	132	1	22
β-strand	138-141	4	23
α-helix	143-145	3
α-helix	149-153	5
β-strand	165-166	2	23
β-strand	173-176	4	23
α-helix	191-199	9

Chain G: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-25	14	24
β-strand	28-40	13	24
β-strand	45-53	9	24
α-helix	56-69	14
β-strand	71-73	3	24
β-strand	77	1	25
β-strand	80	1	25
β-strand	85-89	5	26
β-strand	92-98	7	26
β-strand	105-106	2	26
α-helix	110-118	9
β-strand	123-127	5	26
α-helix	133-145	13
α-helix	150-157	8

Chain H: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-15	4
α-helix	21-30	10
β-strand	32	1	27
β-strand	35	1	27
α-helix	36-54	19
α-helix	58-69	12
β-strand	73-78	6	28
β-strand	85-90	6	28
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-128	13
α-helix	134-147	14

Chain I: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	29
α-helix	31-43	13
β-strand	46-52	7	29
β-strand	59-64	6	29
β-strand	66-67	2	30
β-strand	71-72	2	30
β-strand	77-79	3	31
β-strand	82	1	32
β-strand	85	1	32
β-strand	88-89	2	31
α-helix	94-96	3
α-helix	98-100	3
β-strand	103-107	5	31
β-strand	112-113	2	31
α-helix	115-120	6
β-strand	125-131	7	31

Chain J: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	33
β-strand	15-23	9	33
β-strand	28-30	3	33
β-strand	34	1	33
α-helix	35-38	4
α-helix	42-54	13
β-strand	61-68	8	33
α-helix	72-90	19
α-helix	92-94	3
α-helix	95-100	6

12 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	9	Bacillus subtilis subsp. subtilis str. 168
Ribonuclease R	C	protein	779	Bacillus subtilis subsp. subtilis str. 168	O32231 (AlphaFold model)
30S ribosomal protein S2	D	protein	246	Bacillus subtilis subsp. subtilis str. 168	P21464 (AlphaFold model)
30S ribosomal protein S3	E	protein	218	Bacillus subtilis subsp. subtilis str. 168	P21465 (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
30S ribosomal protein S7	H	protein	156	Bacillus subtilis subsp. subtilis str. 168	P21469
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 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

10 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8CDU_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

>8CDU_2 RNA Substrate (chains B)
AAAAAAAAA

Sequence of entity 3 (C), FASTA

>8CDU_3 Ribonuclease R (chains C)
MEKEAFMEKLLSFMKEEAYKPLTVQELEEMLNITEAEEFKELVKALVALEEKGLIVRTRS
DRYGIPEKMNLIKGKISAHAKGFAFLLPEDTSLSDVFIPPNELNTAMNGDIVMVRLNSQS
SGSRQEGTVIRILERAIQRVVGTYTETRNFGFVIPDDKKITSDIFIPKNGKNGAAEGHKV
VVKLTSYPEGRMNAEGEVETILGHKNDPGIDILSVIHKHGLPGEFPADAMEQASSTPDTI
DEKDLKDRRDLRDQVIVTIDGADAKDLDDAVTVTKLDDGSYKLGVHIADVSHYVTENSPI
DKEALERGTSVYLVDRVIPMIPHRLSNGICSLNPKVDRLTLSCEMTINSQGQVTEHEIFQ
SVIKTTERMTYSDVNKILVDDDEELKQKYEPLVPMFKDMERLAQILRDKRMDRGAVDFDF
KEAKVLVDDEGAVKDVVIRERSVAEKLIEEFMLVANETVAEHFHWMNVPFIYRIHEEPNA
EKLQKFLEFVTTFGYVVKGTAGNIHPRALQSILDAVRDRPEETVISTVMLRSMKQAKYDP
QSLGHFGLSTEFYTHFTSPIRRYPDLIVHRLIRTYLINGKVDEATQEKWAERLPDIAEHT
SSMERRAVDAERETDDLKKAEYMLDKIGEEFDGMISSVTNFGMFVELPNTIEGLVHVSFM
TDDYYRFDEQHFAMIGERTGNVFRIGDEITVKVVDVNKDERNIDFEIVGMKGTPRRPREL
DSSRSRKRGKPARKRVQSTNTPVSPAPSEEKGEWFTKPKKKKKKRGFQNAPKQKRKKKK

Sequence of entity 4 (D), FASTA

>8CDU_4 30S ribosomal protein S2 (chains D)
MSVISMKQLLEAGVHFGHQTRRWNPKMKRYIFTERNGIYIIDLQKTVKKVEEAYNFTKNL
AAEGGKILFVGTKKQAQDSVKEEAQRSGMYYVNQRWLGGTLTNFETIQKRIKRLKDIEKM
QENGTFDVLPKKEVVQLKKELERLEKFLGGIKDMKDLPDALFIIDPRKERIAVAEARKLN
IPIIGIVDTNCDPDEIDVVIPANDDAIRAVKLLTSKMADAILEAKQGEEEAEVAEETAPE
TETTTA

Sequence of entity 5 (E), FASTA

>8CDU_5 30S ribosomal protein S3 (chains E)
MGQKVNPVGLRIGVIRDWESKWYAGKDYADFLHEDLKIREYISKRLSDASVSKVEIERAA
NRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIA
RQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRAD
IDYATSEADTTYGKLGVKVWIYRGEVLPTKKKNEEGGK

Sequence of entity 6 (F), FASTA

>8CDU_6 30S ribosomal protein S4 (chains F)
MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHM
YGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHIL
VDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLP
ERSELAPEINEALIVEFYSR

Sequence of entity 7 (G), FASTA

>8CDU_7 30S ribosomal protein S5 (chains G)
MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAI
RKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGV
ADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG

Sequence of entity 8 (H), FASTA

>8CDU_8 30S ribosomal protein S7 (chains H)
MPRKGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKSQTILYKSFDIIKERTGNDAME
VFEQALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERL
ANEILDAANNTGAAVKKREDTHKMAEANKAFAHYRW

Sequence of entity 9 (I), FASTA

>8CDU_9 30S ribosomal protein S8 (chains I)
MVMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGII
RVFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARA
KQAGGEVLAYVW

Sequence of entity 10 (J), FASTA

>8CDU_10 30S ribosomal protein S9 (chains J)
MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGT
YDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKG
ARRAPQFSKR

Sequence of entity 11 (L), FASTA

>8CDU_11 30S ribosomal protein S12 (chains L)
MPTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNS
ALRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGV
ENRAQGRSKYGTKKPKAK

Sequence of entity 12 (M), FASTA

>8CDU_12 30S ribosomal protein S13 (chains M)
MARIAGVDIPRDKRVVISLTYIFGIGRTTAQQVLKEAGVSEDTRVRDLTEEELGKIRDII
DKLKVEGDLRREVSLNIKRLIEIGSYRGIRHRRGLPVRGQNSKNNARTRKGPRRTVANKK
K

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:

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)
8CDV 4.73 Å, Rnase R bound to a 30S degradation intermediate (state II)

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