[English] 日本語
Yorodumi- PDB-3j9w: Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j9w | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex | ||||||
Components |
| ||||||
Keywords | RIBOSOME / stalling / translation arrest / mifm / L22 | ||||||
Function / homology | Function and homology information positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / membrane => GO:0016020 / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Sohmen, D. / Chiba, S. / Shimokawa-Chiba, N. / Innis, C.A. / Berninghausen, O. / Beckmann, R. / Ito, K. / Wilson, D.N. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Authors: Daniel Sohmen / Shinobu Chiba / Naomi Shimokawa-Chiba / C Axel Innis / Otto Berninghausen / Roland Beckmann / Koreaki Ito / Daniel N Wilson / 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 ...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. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j9w.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3j9w.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3j9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j9w_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3j9w_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 3j9w_validation.xml.gz | 307.7 KB | Display | |
Data in CIF | 3j9w_validation.cif.gz | 500.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9w ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9w | HTTPS FTP |
-Related structure data
Related structure data | 6306MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 5 types, 5 molecules AAAXAYBABB
#1: RNA chain | Mass: 503698.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
---|---|
#21: RNA chain | Mass: 24815.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#22: RNA chain | Mass: 6204.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#33: RNA chain | Mass: 949606.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
#34: RNA chain | Mass: 38423.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
-30S ribosomal protein ... , 19 types, 19 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASAT
#2: Protein | Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21464 |
---|---|
#3: Protein | Mass: 24364.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21465 |
#4: Protein | Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21466 |
#5: Protein | Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21467 |
#6: Protein | Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21468 |
#7: Protein | Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21469 |
#8: Protein | Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12879 |
#9: Protein | Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21470 |
#10: Protein | Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21471 |
#11: Protein | Mass: 13952.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P04969 |
#12: Protein | Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21472 |
#13: Protein | Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P20282 |
#14: Protein | Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12878 |
#15: Protein | Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21473 |
#16: Protein | Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21474 |
#17: Protein | Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12874 |
#18: Protein | Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21475 |
#19: Protein | Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21476 |
#20: Protein | Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21477 |
-Protein , 1 types, 1 molecules AZ
#23: Protein | Mass: 11156.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: Q7WY64 |
---|
+50S ribosomal protein ... , 29 types, 29 molecules B0B1B2B3B4B5B6B7B8BDBEBFBGBHBJBKBMBNBOBPBQBRBSBTBUBVBWBXBZ
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer solution | pH: 7.2 | ||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 2 nm pre-coated Quantifoil R3/3 holey carbon support grids | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Date: Apr 12, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 125085 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 0 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: defocus groups | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305045 / Nominal pixel size: 1.108 Å / Actual pixel size: 1.108 Å Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A ...Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012). (Single particle--Applied symmetry: C1) Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
|