5NJT: 30S ribosomal protein S2

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. Determined by electron microscopy at 3.8 Å resolution. Released 14 Jun 2017.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 51
Atoms: 133,097
Mol. weight: 2111.7 kDa
Released: 14 Jun 2017

Explore 5NJT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NJT contains 196 α-helices and 308 β-strands across 48 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	1
β-strand	17	1	2
β-strand	24-27	4	2
β-strand	34-37	4	2
β-strand	43	1	3
β-strand	46-47	2	1
β-strand	50-51	2	1
β-strand	54	1	3
α-helix	60-76	17
α-helix	77-79	3
β-strand	84-89	6	4
β-strand	91	1	5
β-strand	97-100	4	6
β-strand	103-106	4	6
β-strand	114-116	3	6
β-strand	123-125	3	4
β-strand	131-136	6	4
α-helix	139-150	12
β-strand	162	1	5
β-strand	165	1	4

Chain b: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	6-13	8
α-helix	16-19	4
α-helix	34-45	12
α-helix	75-77	3
α-helix	95-97	3

Chain B: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	26-28	3
β-strand	31-34	4	7
β-strand	39-41	3	7
α-helix	42	1
α-helix	43-61	19
β-strand	67-70	4	8
α-helix	77-85	9
β-strand	92	1	8
α-helix	96-97	2
α-helix	100-103	4
α-helix	106-119	14
α-helix	131-142	12
α-helix	145-148	4
α-helix	150-153	4
β-strand	160-163	4	8
α-helix	170-178	9
β-strand	184-185	2	9
α-helix	193-195	3
β-strand	198-199	2	9
α-helix	207-225	19

Chain c: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	14
α-helix	30-38	9
β-strand	55-58	4	14
β-strand	74-76	3	15
β-strand	87-89	3	15
α-helix	90-95	6
α-helix	99-109	11
α-helix	111	1
α-helix	118-122	5
β-strand	124-125	2	14
α-helix	134-136	3
β-strand	139-140	2	14

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	12	1	10
β-strand	16	1	10
β-strand	21	1	11
α-helix	28-45	18
β-strand	54-58	5	11
β-strand	63-67	5	11
α-helix	73-76	4
α-helix	81-94	14
α-helix	112-121	10
α-helix	129-139	11
β-strand	147-151	5	12
β-strand	166-170	5	12
β-strand	182-185	4	12
β-strand	189	1	13
β-strand	194	1	13
β-strand	198-202	5	12
α-helix	205-208	4

Chain d: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	17
β-strand	12	1	18
β-strand	16-24	9	17
β-strand	38-46	9	17
β-strand	60-61	2	17
β-strand	68-70	3	19
β-strand	76-79	4	19
β-strand	85-86	2	17
β-strand	87	1	20
β-strand	93	1	20
β-strand	98	1	18
β-strand	101-102	2	21
α-helix	104-108	5
α-helix	112-116	5
β-strand	120-121	2	21

Chain D: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	46-59	14
α-helix	65-76	12
α-helix	82-89	8
α-helix	94-99	6
α-helix	107-114	8
α-helix	149-156	8
β-strand	165-166	2	16
β-strand	175-176	2	16
α-helix	192-196	5

Chain e: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	38-40	3
β-strand	78	1	28
α-helix	79-84	6
β-strand	91	1	29
α-helix	93-97	5
β-strand	112	1	28
β-strand	123-125	3	29
α-helix	132-139	8
β-strand	143-145	3	29

40 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 ribosomal RNA	A	RNA	1544	Bacillus subtilis subsp. subtilis str. 168
30S ribosomal protein S2	B	protein	224	Bacillus subtilis subsp. subtilis str. 168	P21464 (AlphaFold model)
30S ribosomal protein S3	C	protein	210	Bacillus subtilis subsp. subtilis str. 168	P21465 (AlphaFold model)
30S ribosomal protein S4	D	protein	199	Bacillus subtilis subsp. subtilis str. 168	P21466 (AlphaFold model)
30S ribosomal protein S5	E	protein	165	Bacillus subtilis subsp. subtilis str. 168	P21467 (AlphaFold model)
30S ribosomal protein S6	F	protein	95	Bacillus subtilis subsp. subtilis str. 168	P21468
30S ribosomal protein S7	G	protein	153	Bacillus subtilis subsp. subtilis str. 168	P21469
30S ribosomal protein S8	H	protein	131	Bacillus subtilis subsp. subtilis str. 168	P12879
30S ribosomal protein S9	I	protein	130	Bacillus subtilis subsp. subtilis str. 168	P21470
30S ribosomal protein S10	J	protein	102	Bacillus subtilis subsp. subtilis str. 168	P21471
30S ribosomal protein S11	K	protein	118	Bacillus subtilis subsp. subtilis str. 168	P04969
30S ribosomal protein S12	L	protein	137	Bacillus subtilis subsp. subtilis str. 168	P21472

39 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5NJT_1 16S ribosomal RNA (chains A)
GGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGA
GCGGACAGAUGGGAGCUUGCUCCCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGGU
AACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGGUUGUUU
GAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGACCCGCGG
CGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUGCGUAGCCGACCUGAG
AGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUA
GGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUU
UUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUGCCGUUCGAAUAGGGCGGUACC
UUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGU
AGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUCUUAAGU
CUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACUUGAGUG
CAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACA
CCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAG
CGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGG
GGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUC
GCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUU
AAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCUAGAGAU
AGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCG
UGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAGCAUUCA
GUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAA
UCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAAGGGCAG
CGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAGUCUGCA
ACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUAC
GUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCG
GUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUGAAGUCG
UAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUU

Sequence of entity 2 (B), FASTA

>5NJT_2 30S ribosomal protein S2 (chains B)
MKQLLEAGVHFGHQTRRWNPKMKRYIFTERNGIYIIDLQKTVKKVEEAYNFTKNLAAEGG
KILFVGTKKQAQDSVKEEAQRSGMYYVNQRWLGGTLTNFETIQKRIKRLKDIEKMQENGT
FDVLPKKEVVQLKKELERLEKFLGGIKDMKDLPDALFIIDPRKERIAVAEARKLNIPIIG
IVDTNCDPDEIDVVIPANDDAIRAVKLLTSKMADAILEAKQGEE

Sequence of entity 3 (C), FASTA

>5NJT_3 30S ribosomal protein S3 (chains C)
GQKVNPVGLRIGVIRDWESKWYAGKDYADFLHEDLKIREYISKRLSDASVSKVEIERAAN
RVNITIHTAKPGMVIGKGGSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIAR
QLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRADI
DYATSEADTTYGKLGVKVWIYRGEVLPTKK

Sequence of entity 4 (D), FASTA

>5NJT_4 30S ribosomal protein S4 (chains D)
ARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHMY
GVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHILV
DGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLPE
RSELAPEINEALIVEFYSR

Sequence of entity 5 (E), FASTA

>5NJT_5 30S ribosomal protein S5 (chains E)
RRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAIR
KAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGVA
DILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG

Sequence of entity 6 (F), FASTA

>5NJT_6 30S ribosomal protein S6 (chains F)
MRKYEVMYIIRPNIDEESKKAVIERFNNVLTSNGAEITGTKDWGKRRLAYEINDFRDGFY
QIVNVQSDAAAVQEFDRLAKISDDIIRHIVVKEEE

Sequence of entity 7 (G), FASTA

>5NJT_7 30S ribosomal protein S7 (chains G)
KGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKSQTILYKSFDIIKERTGNDAMEVFE
QALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERLANE
ILDAANNTGAAVKKREDTHKMAEANKAFAHYRW

Sequence of entity 8 (H), FASTA

>5NJT_8 30S ribosomal protein S8 (chains H)
VMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGIIR
VFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARAK
QAGGEVLAYVW

Sequence of entity 9 (I), FASTA

>5NJT_9 30S ribosomal protein S9 (chains I)
MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGT
YDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKG
ARRAPQFSKR

Sequence of entity 10 (J), FASTA

>5NJT_10 30S ribosomal protein S10 (chains J)
MAKQKIRIRLKAYDHRILDQSAEKIVETAKRSGASVSGPIPLPTEKSVYTILRAVHKYKD
SREQFEMRTHKRLIDIVNPTPQTVDALMRLDLPSGVDIEIKL

Sequence of entity 11 (K), FASTA

>5NJT_11 30S ribosomal protein S11 (chains K)
RRVKKNIESGIAHIRSTFNNTIVTITDTHGNAISWSSAGALGFRGSRKSTPFAAQMAAET
AAKGSIEHGLKTLEVTVKGPGSGREAAIRALQAAGLEVTAIRDVTPVPHNGCRPPKRR

Sequence of entity 12 (L), FASTA

>5NJT_12 30S ribosomal protein S12 (chains L)
PTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNSA
LRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVE
NRAQGRSKYGTKKPKAK

Primary citation

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. Beckert, B., Abdelshahid, M., Schafer, H. et al. EMBO J (2017) 36:2061-2072. DOI 10.15252/embj.201696189 · PubMed

Other PDB entries of the same protein (UniProt P21464 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FY1 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in…
9FY2 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
9FY3 2.8 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
8BUU 2.9 Å, ARE-ABCF VmlR2 bound to a 70S ribosome
6HA1 3.1 Å, Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader…
8CDU 3.1 Å, Rnase R bound to a 30S degradation intermediate (main state)
7O5B 3.33 Å, Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex…
8QPP 3.4 Å, Bacillus subtilis MutS2-collided disome complex (stalled 70S)
6HA8 3.5 Å, Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome
7QV2 3.5 Å, Bacillus subtilis collided disome (Collided 70S)
8CEC 3.57 Å, Rnase R bound to a 30S degradation intermediate (State I - head-turning)
8R55 3.57 Å, Bacillus subtilis MutS2-collided disome complex (collided 70S)

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