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- PDB-6emg: Crystal structure of Rrp1 from Chaetomium thermophilum in space g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6emg | ||||||
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Title | Crystal structure of Rrp1 from Chaetomium thermophilum in space group P6322 | ||||||
![]() | G0S4M2 | ||||||
![]() | RIBOSOME / Ribosome biogenesis / translation | ||||||
Function / homology | Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / preribosome, small subunit precursor / rRNA processing / nucleus / PHOSPHATE ION / Ribosomal RNA-processing protein 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ahmed, Y.L. / Sinning, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann / ![]() Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.6 KB | Display | ![]() |
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PDB format | ![]() | 171 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.2 KB | Display | ![]() |
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Full document | ![]() | 478.4 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3888C ![]() 3889C ![]() 3890C ![]() 3891C ![]() 3892C ![]() 3893C ![]() 6elzC ![]() 6em1C ![]() 6em3C ![]() 6em4C ![]() 6em5C ![]() 6emfC ![]() 6en7C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33101.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0031510 / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.24 Å3/Da / Density % sol: 80.3 % / Description: hexagonal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.8M K-H2PO4 0.8M Na-H2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99188 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→49.222 Å / Num. obs: 80956 / % possible obs: 99.96 % / Redundancy: 20.2 % / Biso Wilson estimate: 47.48 Å2 / Net I/σ(I): 24.62 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 220.2 Å2 / Biso mean: 69.141 Å2 / Biso min: 29.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.24→49.222 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 62.8368 Å / Origin y: 71.1197 Å / Origin z: 18.2993 Å
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Refinement TLS group |
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