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- PDB-3j2e: Dissecting the in vivo assembly of the 30S ribosomal subunit reve... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3j2e | ||||||
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Title | Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM | ||||||
![]() | 16S rRNA | ||||||
![]() | RIBOSOME / Ribosome biogenesis / 30S subunit assembly / RimM | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15.3 Å | ||||||
![]() | Guo, Q. / Goto, S. / Chen, Y. / Muto, A. / Himeno, H. / Deng, H. / Lei, J. / Gao, N. | ||||||
![]() | ![]() Title: Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process. Authors: Qiang Guo / Simon Goto / Yuling Chen / Boya Feng / Yanji Xu / Akira Muto / Hyouta Himeno / Haiteng Deng / Jianlin Lei / Ning Gao / ![]() Abstract: Ribosome biogenesis is a tightly regulated, multi-stepped process. The assembly of ribosomal subunits is a central step of the complex biogenesis process, involving nearly 30 protein factors in vivo ...Ribosome biogenesis is a tightly regulated, multi-stepped process. The assembly of ribosomal subunits is a central step of the complex biogenesis process, involving nearly 30 protein factors in vivo in bacteria. Although the assembly process has been extensively studied in vitro for over 40 years, very limited information is known for the in vivo process and specific roles of assembly factors. Such an example is ribosome maturation factor M (RimM), a factor involved in the late-stage assembly of the 30S subunit. Here, we combined quantitative mass spectrometry and cryo-electron microscopy to characterize the in vivo 30S assembly intermediates isolated from mutant Escherichia coli strains with genes for assembly factors deleted. Our compositional and structural data show that the assembly of the 3'-domain of the 30S subunit is severely delayed in these intermediates, featured with highly underrepresented 3'-domain proteins and large conformational difference compared with the mature 30S subunit. Further analysis indicates that RimM functions not only to promote the assembly of a few 3'-domain proteins but also to stabilize the rRNA tertiary structure. More importantly, this study reveals intriguing similarities and dissimilarities between the in vitro and the in vivo assembly pathways, suggesting that they are in general similar but with subtle differences. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 806.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5507MC ![]() 5500C ![]() 5501C ![]() 5502C ![]() 5503C ![]() 5504C ![]() 5506C ![]() 5508C ![]() 5509C ![]() 5510C ![]() 3j28C ![]() 3j29C ![]() 3j2aC ![]() 3j2bC ![]() 3j2cC ![]() 3j2dC ![]() 3j2fC ![]() 3j2gC ![]() 3j2hC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: RNA chain | Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Name immature ribosomal small subunit from rimM gene deleted E.coli strain treated with RimM in vitro Type: RIBOSOME |
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Molecular weight | Value: 0.8 MDa / Experimental value: NO |
Buffer solution | pH: 7.5 / Details: 150 mM NH4Cl,10mM Tris-HCL,10mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 150 mM NH4Cl,10mM Tris-HCL,10mM MgCl2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 1 seconds before plunging |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jan 1, 2012 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1500 nm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: Weiner filter | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: Reference Projections / Resolution: 15.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 29012 Details: (Details about the particle: This is a classification volume (No. 2) using ML3D methods.) Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation Details: REFINEMENT PROTOCOL--Initial local fitting was done using Chimera and then MDFF was used for flexible fitting DETAILS--ref- Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and Schulten, K. ...Details: REFINEMENT PROTOCOL--Initial local fitting was done using Chimera and then MDFF was used for flexible fitting DETAILS--ref- Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and Schulten, K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16, 673-683 | ||||||||||||
Atomic model building | PDB-ID: 3OFA![]() 3ofa Pdb chain-ID: A / Accession code: 3OFA / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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