3J9W image
Deposition Date 2015-03-16
Release Date 2015-04-29
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3J9W
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex
Biological Source:
Source Organism:
Bacillus subtilis subsp. subtilis str. 168 (Taxon ID: 224308)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
3J9W validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA)
Chain Length:1555
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21464 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC)
Chain Length:218
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21465 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD)
Chain Length:200
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21466 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21467 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein bS6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21468 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG)
Chain Length:156
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21469 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS8
Gene (Uniprot):rpsH
Chain IDs:H (auth: AH)
Chain Length:132
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12879 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI)
Chain Length:130
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21470 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21471 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P04969 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21472 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20282 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS14
Gene (Uniprot):rpsN1
Chain IDs:N (auth: AN)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12878 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO)
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21473 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein bS16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP)
Chain Length:90
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21474 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: AQ)
Chain Length:87
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12874 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein bS18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR)
Chain Length:79
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21475 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein uS19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21476 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein bS20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21477 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:tRNA-Asp
Chain IDs:U (auth: AX)
Chain Length:77
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:V (auth: AY)
Chain Length:19
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:MifM
Gene (Uniprot):mifM
Chain IDs:W (auth: AZ)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:Q7WY64
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL28
Gene (Uniprot):rpmB
Chain IDs:X (auth: B0)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P37807 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL29
Gene (Uniprot):rpmC
Chain IDs:Y (auth: B1)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12873 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL30
Gene (Uniprot):rpmD
Chain IDs:Z (auth: B2)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P19947 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL31
Gene (Uniprot):rpmE
Chain IDs:AA (auth: B3)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:Q03223 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL32
Gene (Uniprot):rpmF
Chain IDs:BA (auth: B4)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:O34687 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL33
Gene (Uniprot):rpmGA
Chain IDs:CA (auth: B5)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P56849 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL34
Gene (Uniprot):rpmH
Chain IDs:DA (auth: B6)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P05647 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL35
Gene (Uniprot):rpmI
Chain IDs:EA (auth: B7)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P55874 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL36
Gene (Uniprot):rpmJ
Chain IDs:FA (auth: B8)
Chain Length:37
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20278 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:GA (auth: BA)
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:HA (auth: BB)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL2
Gene (Uniprot):rplB
Chain IDs:IA (auth: BD)
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42919 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL3
Gene (Uniprot):rplC
Chain IDs:JA (auth: BE)
Chain Length:209
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42920 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL4
Gene (Uniprot):rplD
Chain IDs:KA (auth: BF)
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42921 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL5
Gene (Uniprot):rplE
Chain IDs:LA (auth: BG)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12877 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL6
Gene (Uniprot):rplF
Chain IDs:MA (auth: BH)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P46898 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL10
Gene (Uniprot):rplJ
Chain IDs:NA (auth: BJ)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42923 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL11
Gene (Uniprot):rplK
Chain IDs:OA (auth: BK)
Chain Length:141
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:Q06796 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL13
Gene (Uniprot):rplM
Chain IDs:PA (auth: BM)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P70974 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL14
Gene (Uniprot):rplN
Chain IDs:QA (auth: BN)
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12875 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL15
Gene (Uniprot):rplO
Chain IDs:RA (auth: BO)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P19946 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL16
Gene (Uniprot):rplP
Chain IDs:SA (auth: BP)
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P14577 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL17
Gene (Uniprot):rplQ
Chain IDs:TA (auth: BQ)
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20277 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL18
Gene (Uniprot):rplR
Chain IDs:UA (auth: BR)
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P46899 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL19
Gene (Uniprot):rplS
Chain IDs:VA (auth: BS)
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:O31742 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL20
Gene (Uniprot):rplT
Chain IDs:WA (auth: BT)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P55873 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL21
Gene (Uniprot):rplU
Chain IDs:XA (auth: BU)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P26908 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL22
Gene (Uniprot):rplV
Chain IDs:YA (auth: BV)
Chain Length:113
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42060 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL23
Gene (Uniprot):rplW
Chain IDs:ZA (auth: BW)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42924 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL24
Gene (Uniprot):rplX
Chain IDs:AB (auth: BX)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P0CI78 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL27
Gene (Uniprot):rpmA
Chain IDs:BB (auth: BZ)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P05657 Pfam ID:PF01016
Ligand Molecules
NA
Primary Citation
Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Nat Commun 6 6941 6941 (2015)
PMID: 25903689 DOI: 10.1038/ncomms7941

Abstact

Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5-3.9 Å, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner.

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Protein

Chemical

Disease

Primary Citation of related structures
3J9W
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