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Yorodumi- PDB-8j8q: Structure of the four-component Paf1 complex from Saccharomyces e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j8q | |||||||||
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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: 3.11 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 | 8j8q.cif.gz | 498 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j8q.ent.gz | 370.4 KB | Display | PDB format |
PDBx/mmJSON format | 8j8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/8j8q ftp://data.pdbj.org/pub/pdb/validation_reports/j8/8j8q | HTTPS FTP |
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-Related structure data
Related structure data | 8j8pC 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: 105524.789 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: 12841.327 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 |
#3: Protein | Mass: 9468.526 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 |
#4: Protein | Mass: 8535.536 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 |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.68 % |
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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: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX170-HS / Detector: CCD / Date: Oct 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 28686 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.08 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.7→3.15 Å / Rmerge(I) obs: 1.116 / Num. unique obs: 1421 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.11→27.07 Å / SU ML: 0.3946 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.1256 / 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: 71.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.11→27.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.1641781077 Å / Origin y: 33.1082699959 Å / Origin z: -5.91981776579 Å
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Refinement TLS group | Selection details: all |