+Open data
-Basic information
Entry | Database: PDB / ID: 6en7 | ||||||
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Title | Crystal structure of the ribosome assembly factor Nsa1 | ||||||
Components | Ribosome biogenesis protein NSA1 | ||||||
Keywords | CHAPERONE / Ribosome / biogenesis | ||||||
Function / homology | WDR74/Nsa1 / preribosome, large subunit precursor / ribosomal large subunit biogenesis / rRNA processing / WD40-repeat-containing domain superfamily / nucleolus / nucleus / Ribosome biogenesis protein NSA1 Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å | ||||||
Authors | Altegoer, F. / Bange, G. | ||||||
Citation | Journal: Cell / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6en7.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6en7.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 6en7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6en7_validation.pdf.gz | 419.9 KB | Display | wwPDB validaton report |
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Full document | 6en7_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 6en7_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6en7_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/6en7 ftp://data.pdbj.org/pub/pdb/validation_reports/en/6en7 | HTTPS FTP |
-Related structure data
Related structure data | 3888C 3889C 3890C 3891C 3892C 3893C 6elzC 6em1C 6em3C 6em4C 6em5C 6emfC 6emgC 5sumS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51982.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NSA1, YGL111W, G2990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53136 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 25% w/v PEG-1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→59.5 Å / Num. obs: 15750 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04384 / Net I/σ(I): 34.78 |
Reflection shell | Resolution: 2.4→2.489 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.1126 / Mean I/σ(I) obs: 14.02 / Num. unique obs: 1543 / CC1/2: 0.992 / % possible all: 99.23 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5SUM Resolution: 2.403→46.408 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 19.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.403→46.408 Å
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Refine LS restraints |
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LS refinement shell |
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