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Yorodumi- PDB-8j8p: Structure of the four-component Paf1 complex from Saccharomyces e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j8p | |||||||||
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Title | Structure of the four-component Paf1 complex from Saccharomyces eubayanus | |||||||||
Components |
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Keywords | TRANSCRIPTION / transcription elongation factor / the polymerase associated factor 1 (Paf1) complex | |||||||||
Function / homology | Function and homology information : / Cdc73/Paf1 complex / transcription elongation by RNA polymerase II / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces eubayanus (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | |||||||||
Authors | Wang, Z. / Qin, Y. / Zhou, Y. / Cao, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Basis of the Transcriptional Elongation Factor Paf1 Core Complex from Saccharomyces eubayanus . Authors: Qin, Y. / Zhou, Y. / Cao, Y. / Ren, Y. / Deng, P. / Jiang, J. / Wang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j8p.cif.gz | 241.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j8p.ent.gz | 187.6 KB | Display | PDB format |
PDBx/mmJSON format | 8j8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j8p_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 8j8p_full_validation.pdf.gz | 516.3 KB | Display | |
Data in XML | 8j8p_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 8j8p_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/8j8p ftp://data.pdbj.org/pub/pdb/validation_reports/j8/8j8p | HTTPS FTP |
-Related structure data
Related structure data | 8j8qC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 104814.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_2263 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RHL9 |
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#2: Protein | Mass: 8488.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_3914 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RF82 |
#3: Protein | Mass: 12700.642 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_1302 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RM45 |
#4: Protein | Mass: 9374.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_1738 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RIY1 |
#5: 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: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium citrate tribasic pH 7.0; 25% w/v Polyethylene glyco 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 43763 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 64.74 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. unique obs: 2197 / CC1/2: 0.706 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→34.47 Å / SU ML: 0.3742 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.1952 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→34.47 Å
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Refine LS restraints |
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LS refinement shell |
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