3J9W: Bacillus subtilis MifM-stalled ribosome complex

Name: PDB 3J9W: Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex
Published: 2015-04-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex. Determined by electron microscopy at 3.9 Å resolution. Released 29 Apr 2015.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Bacillus subtilis subsp. subtilis str. 168
Chains: 54
Atoms: 135,425
Mol. weight: 2185.4 kDa
Released: 29 Apr 2015

Explore 3J9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J9W contains 245 α-helices and 310 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 AB: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	25-27	3
β-strand	31-34	4	7
β-strand	39-41	3	7
α-helix	43-63	21
β-strand	67-69	3	8
α-helix	77-87	11
β-strand	91	1	8
α-helix	96-97	2
α-helix	105-120	16
α-helix	131-148	18
α-helix	151-153	3
α-helix	157-158	2
β-strand	160-162	3	8
α-helix	170-178	9
β-strand	183	1	8
β-strand	184-187	4	9
α-helix	193-195	3
β-strand	198-201	4	9
α-helix	207-224	18

Chain AC: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	16
β-strand	16	1	16
β-strand	20-21	2	17
α-helix	28-45	18
β-strand	53-55	3	18
β-strand	56-57	2	17
β-strand	58	1	19
β-strand	63	1	19
β-strand	66-68	3	18
α-helix	73-76	4
α-helix	81-94	14
α-helix	108-110	3
α-helix	112-124	13
α-helix	129-143	15
β-strand	147-154	8	20
β-strand	156	1	21
β-strand	159	1	21
β-strand	164-170	7	20
β-strand	181-189	9	20
β-strand	194-202	9	20
α-helix	205-208	4

Chain AD: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	32	1
α-helix	40-45	6
α-helix	46-61	16
α-helix	65-77	13
α-helix	82-90	9
β-strand	93	1	23
α-helix	94-100	7
α-helix	107-116	10
β-strand	120-121	2	24
β-strand	124-125	2	24
β-strand	132	1	23
β-strand	138-140	3	24
α-helix	143-145	3
α-helix	149-156	8
α-helix	160-162	3
β-strand	165-168	4	24
β-strand	173-176	4	24
α-helix	179-181	3
α-helix	191-197	7

Chain AE: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	15-25	11	25
β-strand	28-40	13	25
β-strand	46-53	8	25
α-helix	56-69	14
β-strand	72	1	25
β-strand	85-86	2	26
β-strand	92-97	6	26
β-strand	105	1	27
α-helix	109-118	10
β-strand	123	1	27
β-strand	124-129	6	26
α-helix	133-146	14
α-helix	150-156	7

Chain AF: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	29
α-helix	16-32	17
β-strand	36-47	12	29
β-strand	57-67	11	29
α-helix	71-81	11
β-strand	85-92	8	29

Chain AG: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-15	6
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-68	11
β-strand	73-74	2	31
β-strand	77-78	2	32
β-strand	85-86	2	32
β-strand	89-90	2	31
α-helix	91-92	2
α-helix	93-109	17
α-helix	116-128	13
α-helix	132-144	13
α-helix	150-152	3

Chain AH: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	24-27	4	33
α-helix	31-43	13
β-strand	46-51	6	33
β-strand	60-64	5	33
β-strand	77-78	2	34
β-strand	82	1	35
β-strand	85	1	35
β-strand	103-108	6	34
β-strand	111-114	4	34
α-helix	115-121	7
β-strand	127-131	5	34

Chain AI: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	36
β-strand	16-22	7	36
β-strand	28-30	3	36
β-strand	33-34	2	36
α-helix	35-38	4
α-helix	44-54	11
β-strand	62-68	7	36
α-helix	72-90	19
α-helix	92-94	3
α-helix	95-101	7
α-helix	111-115	5

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	AA	RNA	1555	Bacillus subtilis subsp. subtilis str. 168
30S ribosomal protein uS2	AB	protein	246	Bacillus subtilis subsp. subtilis str. 168	P21464 (AlphaFold model)
30S ribosomal protein uS3	AC	protein	218	Bacillus subtilis subsp. subtilis str. 168	P21465 (AlphaFold model)
30S ribosomal protein uS4	AD	protein	200	Bacillus subtilis subsp. subtilis str. 168	P21466 (AlphaFold model)
30S ribosomal protein uS5	AE	protein	166	Bacillus subtilis subsp. subtilis str. 168	P21467 (AlphaFold model)
30S ribosomal protein bS6	AF	protein	95	Bacillus subtilis subsp. subtilis str. 168	P21468
30S ribosomal protein uS7	AG	protein	156	Bacillus subtilis subsp. subtilis str. 168	P21469
30S ribosomal protein uS8	AH	protein	132	Bacillus subtilis subsp. subtilis str. 168	P12879
30S ribosomal protein uS9	AI	protein	130	Bacillus subtilis subsp. subtilis str. 168	P21470
30S ribosomal protein uS10	AJ	protein	102	Bacillus subtilis subsp. subtilis str. 168	P21471
30S ribosomal protein uS11	AK	protein	131	Bacillus subtilis subsp. subtilis str. 168	P04969
30S ribosomal protein uS12	AL	protein	138	Bacillus subtilis subsp. subtilis str. 168	P21472

42 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>3J9W_1 16S ribosomal RNA (chains AA)
AUUUAUCGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGC
AAGUCGAGCGGACAGAUGGGAGCUUGCUCCCUGAUGUUAGCGGCGGACGGGUGAGUAACA
CGUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUG
GUUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGA
CCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUGCGUAGCCG
ACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGC
AGCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAU
GAAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUGCCGUUCGAAUAGGG
CGGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGU
AAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUU
CUUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAAC
UUGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGG
AGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCG
UGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGU
GUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAG
UACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAU
GUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCC
UAGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCU
CGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCA
GCAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGA
CGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAA
AGGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCA
GUCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGG
UGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCC
GAAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGU
GAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCUA

Sequence of entity 2 (AB), FASTA

>3J9W_2 30S ribosomal protein uS2 (chains AB)
MSVISMKQLLEAGVHFGHQTRRWNPKMKRYIFTERNGIYIIDLQKTVKKVEEAYNFTKNL
AAEGGKILFVGTKKQAQDSVKEEAQRSGMYYVNQRWLGGTLTNFETIQKRIKRLKDIEKM
QENGTFDVLPKKEVVQLKKELERLEKFLGGIKDMKDLPDALFIIDPRKERIAVAEARKLN
IPIIGIVDTNCDPDEIDVVIPANDDAIRAVKLLTSKMADAILEAKQGEEEAEVAEETAPE
TETTTA

Sequence of entity 3 (AC), FASTA

>3J9W_3 30S ribosomal protein uS3 (chains AC)
MGQKVNPVGLRIGVIRDWESKWYAGKDYADFLHEDLKIREYISKRLSDASVSKVEIERAA
NRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIA
RQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRAD
IDYATSEADTTYGKLGVKVWIYRGEVLPTKKKNEEGGK

Sequence of entity 4 (AD), FASTA

>3J9W_4 30S ribosomal protein uS4 (chains AD)
MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHM
YGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHIL
VDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLP
ERSELAPEINEALIVEFYSR

Sequence of entity 5 (AE), FASTA

>3J9W_5 30S ribosomal protein uS5 (chains AE)
MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAI
RKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGV
ADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG

Sequence of entity 6 (AF), FASTA

>3J9W_6 30S ribosomal protein bS6 (chains AF)
MRKYEVMYIIRPNIDEESKKAVIERFNNVLTSNGAEITGTKDWGKRRLAYEINDFRDGFY
QIVNVQSDAAAVQEFDRLAKISDDIIRHIVVKEEE

Sequence of entity 7 (AG), FASTA

>3J9W_7 30S ribosomal protein uS7 (chains AG)
MPRKGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKSQTILYKSFDIIKERTGNDAME
VFEQALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERL
ANEILDAANNTGAAVKKREDTHKMAEANKAFAHYRW

Sequence of entity 8 (AH), FASTA

>3J9W_8 30S ribosomal protein uS8 (chains AH)
MVMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGII
RVFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARA
KQAGGEVLAYVW

Sequence of entity 9 (AI), FASTA

>3J9W_9 30S ribosomal protein uS9 (chains AI)
MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGT
YDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKG
ARRAPQFSKR

Sequence of entity 10 (AJ), FASTA

>3J9W_10 30S ribosomal protein uS10 (chains AJ)
MAKQKIRIRLKAYDHRILDQSAEKIVETAKRSGASVSGPIPLPTEKSVYTILRAVHKYKD
SREQFEMRTHKRLIDIVNPTPQTVDALMRLDLPSGVDIEIKL

Sequence of entity 11 (AK), FASTA

>3J9W_11 30S ribosomal protein uS11 (chains AK)
MAAARKSNTRKRRVKKNIESGIAHIRSTFNNTIVTITDTHGNAISWSSAGALGFRGSRKS
TPFAAQMAAETAAKGSIEHGLKTLEVTVKGPGSGREAAIRALQAAGLEVTAIRDVTPVPH
NGCRPPKRRRV

Sequence of entity 12 (AL), FASTA

>3J9W_12 30S ribosomal protein uS12 (chains AL)
MPTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNS
ALRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGV
ENRAQGRSKYGTKKPKAK

Primary citation

Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Sohmen, D., Chiba, S., Shimokawa-Chiba, N. et al. Nat Commun (2015) 6:6941-6941. DOI 10.1038/ncomms7941 · 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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