3J9W

Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.

Sohmen, D.Chiba, S.Shimokawa-Chiba, N.Innis, C.A.Berninghausen, O.Beckmann, R.Ito, K.Wilson, D.N.

(2015) Nat Commun 6: 6941-6941

  • DOI: 10.1038/ncomms7941

  • PubMed Abstract: 
  • 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 Bacill ...

    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.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS2
AB
246Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P21464 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21464
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS3
AC
218Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P21465 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21465
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS4
AD
200Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsD
Find proteins for P21466 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21466
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS5
AE
166Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsE (spcA)
Find proteins for P21467 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21467
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein bS6
AF
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P21468 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21468
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS7
AG
156Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P21469 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21469
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS8
AH
132Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P12879 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12879
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS9
AI
130Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P21470 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21470
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS10
AJ
102Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsJ (tetA)
Find proteins for P21471 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21471
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS11
AK
131Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P04969 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P04969
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS12
AL
138Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsL (fun, strA)
Find proteins for P21472 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21472
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS13
AM
121Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P20282 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20282
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS14
AN
61Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsN1 (rpsN, rpsNA, rpsZ)
Find proteins for P12878 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12878
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS15
AO
89Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsO
Find proteins for P21473 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21473
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein bS16
AP
90Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P21474 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21474
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS17
AQ
87Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P12874 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12874
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein bS18
AR
79Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P21475 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21475
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS19
AS
92Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P21476 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21476
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein bS20
AT
88Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsT (yqeO)
Find proteins for P21477 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21477
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
MifM
AZ
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: mifM (yqzJ)
Find proteins for Q7WY64 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q7WY64
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL28
B0
62Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmB (yloT)
Find proteins for P37807 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37807
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL29
B1
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P12873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12873
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL30
B2
59Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P19947 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19947
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL31
B3
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q03223 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q03223
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL32
B4
59Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmF
Find proteins for O34687 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34687
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL33
B5
49Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmGA (rpmG1)
Find proteins for P56849 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P56849
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL34
B6
44Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmH
Find proteins for P05647 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05647
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL35
B7
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P55874 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55874
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL36
B8
37Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P20278 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20278
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL2
BD
277Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplB
Find proteins for P42919 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42919
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL3
BE
209Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplC
Find proteins for P42920 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42920
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL4
BF
207Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplD
Find proteins for P42921 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42921
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL5
BG
179Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplE
Find proteins for P12877 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12877
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL6
BH
179Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplF
Find proteins for P46898 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46898
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL10
BJ
166Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P42923 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42923
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL11
BK
141Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplK (relC, tsp6)
Find proteins for Q06796 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q06796
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL13
BM
145Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplM
Find proteins for P70974 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P70974
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL14
BN
122Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplN
Find proteins for P12875 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12875
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL15
BO
146Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplO
Find proteins for P19946 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19946
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL16
BP
144Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplP
Find proteins for P14577 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P14577
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL17
BQ
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P20277 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20277
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL18
BR
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplR
Find proteins for P46899 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46899
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL19
BS
115Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplS
Find proteins for O31742 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31742
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL20
BT
119Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplT
Find proteins for P55873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55873
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL21
BU
102Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplU
Find proteins for P26908 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P26908
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL22
BV
113Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplV
Find proteins for P42060 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42060
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL23
BW
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplW
Find proteins for P42924 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42924
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL24
BX
103Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplX
Find proteins for P0CI78 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P0CI78
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL27
BZ
94Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P05657 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05657
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1555Bacillus subtilis subsp. subtilis str. 168
Entity ID: 21
MoleculeChainsLengthOrganism
tRNA-AspAX77Bacillus subtilis subsp. subtilis str. 168
Entity ID: 22
MoleculeChainsLengthOrganism
mRNAAY19Bacillus subtilis subsp. subtilis str. 168
Entity ID: 33
MoleculeChainsLengthOrganism
23S ribosomal RNABA2928Bacillus subtilis subsp. subtilis str. 168
Entity ID: 34
MoleculeChainsLengthOrganism
5S ribosomal RNABB119Bacillus subtilis subsp. subtilis str. 168
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection