8CEC: Rnase R

Rnase R bound to a 30S degradation intermediate (State I - head-turning). Determined by electron microscopy at 3.57 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.57 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 22
Atoms: 51,964
Mol. weight: 867.87 kDa
Released: 20 Dec 2023

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

Secondary structure: helices and β-sheets

8CEC contains 122 α-helices and 147 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 a: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-24	12
β-strand	31-33	3	43
β-strand	39	1	44
α-helix	42-44	3
β-strand	48-52	5	43
β-strand	57-61	5	43
β-strand	70	1	44
α-helix	71-74	4

Chain C: 32 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
β-strand	22	1	1
α-helix	24-30	7
α-helix	36-52	17
β-strand	56-57	2	1
β-strand	63-64	2	1
β-strand	71-78	8	2
β-strand	84-88	5	2
α-helix	94-95	2
β-strand	96-98	3	2
α-helix	100-102	3
β-strand	111-116	6	2
α-helix	117	1
α-helix	125	1
β-strand	126-134	9	2
β-strand	139-146	8	3
β-strand	151-155	5	3
α-helix	163	1
β-strand	164-166	3	3
α-helix	168-170	3
α-helix	174-175	2
β-strand	178-184	7	3
β-strand	189	1	4
β-strand	192	1	4
α-helix	193-194	2
β-strand	195-204	10	3
α-helix	210-219	10
α-helix	225-226	2
α-helix	227-235	9
α-helix	242-245	4
β-strand	249-250	2	5
β-strand	257-260	4	5
β-strand	269-275	7	5
β-strand	281-288	8	5
α-helix	290-293	4
α-helix	299-307	9
β-strand	309	1	6
β-strand	311-312	2	7
β-strand	317-318	2	7
α-helix	323-324	2
α-helix	325-329	5
β-strand	337-347	11	5
β-strand	353-364	12	5
β-strand	367-370	4	5
α-helix	371-378	8
α-helix	383-388	6
α-helix	393-413	21
β-strand	422-427	6	8
β-strand	433-439	7	8
α-helix	443-466	24
β-strand	472-474	3	9
β-strand	475	1	10
α-helix	477-479	3
α-helix	480-492	13
α-helix	506-515	10
α-helix	522-530	9
α-helix	534-536	3
β-strand	537-539	3	9
β-strand	545	1	10
β-strand	550	1	10
β-strand	562	1	6
α-helix	563-572	10
α-helix	573-577	5
α-helix	583-623	41
β-strand	630-639	10	11
β-strand	642-646	5	11
β-strand	652-656	5	11
α-helix	657-659	3
β-strand	665-668	4	12
β-strand	673-676	4	12
β-strand	682-684	3	12
β-strand	688-697	10	11
β-strand	702-709	8	11

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	13
α-helix	25-30	6
β-strand	31-35	5	13
β-strand	38-41	4	13
α-helix	43-62	20
β-strand	67-70	4	14
α-helix	77-87	11
β-strand	90-92	3	14
α-helix	104-122	19
α-helix	132-148	17
β-strand	160-164	5	14
α-helix	170-178	9
β-strand	183-187	5	14
β-strand	198-201	4	14
α-helix	207-225	19

Chain F: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	47-61	15
α-helix	65-75	11
α-helix	82-92	11
β-strand	93	1	15
α-helix	94-100	7
α-helix	107-115	9
β-strand	119-121	3	16
β-strand	124-125	2	16
β-strand	132	1	15
β-strand	139-141	3	16
α-helix	143-145	3
α-helix	149-153	5
β-strand	165-166	2	17
β-strand	173	1	16
β-strand	175-176	2	17
α-helix	191-199	9

Chain G: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-24	13	18
β-strand	29-40	12	18
β-strand	45-53	9	18
α-helix	56-69	14
β-strand	71-73	3	18
β-strand	77	1	19
β-strand	80	1	19
β-strand	85-89	5	20
β-strand	92-98	7	20
β-strand	105-106	2	20
α-helix	109-118	10
β-strand	123-127	5	20
α-helix	133-145	13
α-helix	147-149	3
α-helix	150-157	8

Chain H: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	35
β-strand	16	1	35
β-strand	20-21	2	36
α-helix	28-45	18
β-strand	51-57	7	36
β-strand	64-69	6	36
α-helix	72-76	5
α-helix	81-94	14
β-strand	101	1	36
β-strand	104	1	36
α-helix	112-124	13
α-helix	129-143	15
β-strand	147-152	6	37
β-strand	165-170	6	37
β-strand	179-189	11	37
β-strand	194-205	12	37

Chain I: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
β-strand	24-28	5	21
α-helix	31-42	12
β-strand	46-52	7	21
β-strand	59-64	6	21
β-strand	66	1	22
β-strand	72	1	22
β-strand	77-79	3	23
β-strand	88-89	2	23
α-helix	94-96	3
α-helix	98-100	3
β-strand	103-107	5	23
β-strand	112-114	3	23
α-helix	115-121	7
β-strand	125-131	7	23

Chain K: 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	38
β-strand	35	1	38
α-helix	36-54	19
α-helix	58-69	12
β-strand	73-78	6	39
β-strand	85-90	6	39
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-128	13
α-helix	134-147	14

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	7	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 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 S8	I	protein	132	Bacillus subtilis subsp. subtilis str. 168	P12879
30S ribosomal protein S12	L	protein	138	Bacillus subtilis subsp. subtilis str. 168	P21472
30S ribosomal protein S15	O	protein	89	Bacillus subtilis subsp. subtilis str. 168	P21473
30S ribosomal protein S16	P	protein	90	Bacillus subtilis subsp. subtilis str. 168	P21474
30S ribosomal protein S17	Q	protein	87	Bacillus subtilis subsp. subtilis str. 168	P12874
30S ribosomal protein S20	S	protein	88	Bacillus subtilis subsp. subtilis str. 168	P21477

10 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8CEC_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

>8CEC_2 RNA Substrate (chains B)
AAAAAAA

Sequence of entity 3 (C), FASTA

>8CEC_3 Ribonuclease R (chains C)
MEKEAFMEKLLSFMKEEAYKPLTVQELEEMLNITEAEEFKELVKALVALEEKGLIVRTRS
DRYGIPEKMNLIKGKISAHAKGFAFLLPEDTSLSDVFIPPNELNTAMNGDIVMVRLNSQS
SGSRQEGTVIRILERAIQRVVGTYTETRNFGFVIPDDKKITSDIFIPKNGKNGAAEGHKV
VVKLTSYPEGRMNAEGEVETILGHKNDPGIDILSVIHKHGLPGEFPADAMEQASSTPDTI
DEKDLKDRRDLRDQVIVTIDGADAKDLDDAVTVTKLDDGSYKLGVHIADVSHYVTENSPI
DKEALERGTSVYLVDRVIPMIPHRLSNGICSLNPKVDRLTLSCEMTINSQGQVTEHEIFQ
SVIKTTERMTYSDVNKILVDDDEELKQKYEPLVPMFKDMERLAQILRDKRMDRGAVDFDF
KEAKVLVDDEGAVKDVVIRERSVAEKLIEEFMLVANETVAEHFHWMNVPFIYRIHEEPNA
EKLQKFLEFVTTFGYVVKGTAGNIHPRALQSILDAVRDRPEETVISTVMLRSMKQAKYDP
QSLGHFGLSTEFYTHFTSPIRRYPDLIVHRLIRTYLINGKVDEATQEKWAERLPDIAEHT
SSMERRAVDAERETDDLKKAEYMLDKIGEEFDGMISSVTNFGMFVELPNTIEGLVHVSFM
TDDYYRFDEQHFAMIGERTGNVFRIGDEITVKVVDVNKDERNIDFEIVGMKGTPRRPREL
DSSRSRKRGKPARKRVQSTNTPVSPAPSEEKGEWFTKPKKKKKKRGFQNAPKQKRKKKK

Sequence of entity 4 (D), FASTA

>8CEC_4 30S ribosomal protein S2 (chains D)
MSVISMKQLLEAGVHFGHQTRRWNPKMKRYIFTERNGIYIIDLQKTVKKVEEAYNFTKNL
AAEGGKILFVGTKKQAQDSVKEEAQRSGMYYVNQRWLGGTLTNFETIQKRIKRLKDIEKM
QENGTFDVLPKKEVVQLKKELERLEKFLGGIKDMKDLPDALFIIDPRKERIAVAEARKLN
IPIIGIVDTNCDPDEIDVVIPANDDAIRAVKLLTSKMADAILEAKQGEEEAEVAEETAPE
TETTTA

Sequence of entity 5 (F), FASTA

>8CEC_5 30S ribosomal protein S4 (chains F)
MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHM
YGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHIL
VDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLP
ERSELAPEINEALIVEFYSR

Sequence of entity 6 (G), FASTA

>8CEC_6 30S ribosomal protein S5 (chains G)
MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAI
RKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGV
ADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG

Sequence of entity 7 (I), FASTA

>8CEC_7 30S ribosomal protein S8 (chains I)
MVMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGII
RVFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARA
KQAGGEVLAYVW

Sequence of entity 8 (L), FASTA

>8CEC_8 30S ribosomal protein S12 (chains L)
MPTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNS
ALRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGV
ENRAQGRSKYGTKKPKAK

Sequence of entity 9 (O), FASTA

>8CEC_9 30S ribosomal protein S15 (chains O)
MAITQERKNQLINEFKTHESDTGSPEVQIAILTDSINNLNEHLRTHKKDHHSRRGLLKMV
GKRRNLLTYLRNKDVTRYRELINKLGLRR

Sequence of entity 10 (P), FASTA

>8CEC_10 30S ribosomal protein S16 (chains P)
MAVKIRLKRMGAKKSPFYRIVVADSRSPRDGRFIETVGTYNPVAKPAEVKIDEELALKWL
QTGAKPSDTVRNLFSSQGIMEKFHNAKQGK

Sequence of entity 11 (Q), FASTA

>8CEC_11 30S ribosomal protein S17 (chains Q)
MSERNQRKVYQGRVVSDKMDKTITVVVETYKKHTLYGKRVKYSKKFKAHDENNQAKIGDI
VKIMETRPLSATKRFRLVEVVEEAVII

Sequence of entity 12 (S), FASTA

>8CEC_12 30S ribosomal protein S20 (chains S)
MPNIKSAIKRTKTNNERRVHNATIKSAMRTAIKQVEASVANNEADKAKTALTEAAKRIDK
AVKTGLVHKNTAARYKSRLAKKVNGLSA

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)
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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