+Open data
-Basic information
Entry | Database: PDB / ID: 5wy3 | ||||||
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Title | Crystal structure of Chaetomium thermophilum Utp10 middle domain | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | RIBOSOMAL PROTEIN / NUCLEAR PROTEIN / nucleolar protein / components of 90S preribosome | ||||||
Function / homology | Function and homology information t-UTP complex / snoRNA binding / positive regulation of transcription by RNA polymerase I / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Chen, R. / Zhu, X. / Ye, K. | ||||||
Citation | Journal: Elife / Year: 2017 Title: Molecular architecture of the 90S small subunit pre-ribosome. Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye / Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wy3.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wy3.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wy3_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 5wy3_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 5wy3_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 5wy3_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/5wy3 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/5wy3 | HTTPS FTP |
-Related structure data
Related structure data | 6695C 6696C 6697C 5wwnC 5wwoC 5wxlC 5wxmC 5wyjC 5wykC 5wylC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 44242.691 Da / Num. of mol.: 2 / Fragment: UNP residues 472-872 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / Gene: CTHT_0024640 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5L1 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes-Na, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→19.947 Å / Num. obs: 23700 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 20.753 % / Biso Wilson estimate: 121.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.103 / Χ2: 1.397 / Net I/σ(I): 21.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→19.947 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.56 Å2 / Biso mean: 117.7962 Å2 / Biso min: 64.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→19.947 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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