+Open data
-Basic information
Entry | Database: PDB / ID: 5n9j | |||||||||||||||||||||
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Title | Core Mediator of transcriptional regulation | |||||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase II | |||||||||||||||||||||
Function / homology | Function and homology information core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / euchromatin / nuclear envelope / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / euchromatin / nuclear envelope / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 3.4 Å | |||||||||||||||||||||
Authors | Nozawa, K. / Schneider, T.R. / Cramer, P. | |||||||||||||||||||||
Funding support | Germany, France, Japan, 6items
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Citation | Journal: Nature / Year: 2017 Title: Core Mediator structure at 3.4 Angstrom extends model of transcription initiation complex. Authors: Nozawa, K. / Schneider, T.R. / Cramer, P. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n9j.cif.gz | 611.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n9j.ent.gz | 498.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/5n9j ftp://data.pdbj.org/pub/pdb/validation_reports/n9/5n9j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Mediator of RNA polymerase II transcription subunit ... , 14 types, 14 molecules ABCDEGRSUVWXYZ
#1: Protein | Mass: 68020.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med14, pmc1, SPBC1A4.10c, SPBP23A10.01c / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P7Y4 |
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#2: Protein | Mass: 16352.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med10, nut2, SPBC31F10.09c / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P87310 |
#3: Protein | Mass: 15952.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med19, rox3, SPCC1450.05c / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y7N2 |
#4: Protein | Mass: 15821.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med21, srb7, SPBC1604.10 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94376 |
#5: Protein | Mass: 43573.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med7, SPBC14F5.08 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60104 |
#7: Protein | Mass: 27370.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med4, pmc4, SPBC1105.06 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y821 |
#8: Protein | Mass: 16913.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med31, sep10, SPCP31B10.03c / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9USH1 |
#9: Protein | Mass: 24928.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med6, pmc5, SPAC1002.15c / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9US45 |
#10: Protein | Mass: 23360.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med8, sep15, SPBC21.04 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94646 |
#11: Protein | Mass: 12644.226 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med11, SPAC644.10 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P6Q0 |
#12: Protein | Mass: 62551.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med17, srb4, SPBC31F10.04c / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P87306 |
#13: Protein | Mass: 24345.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med18, pmc6, sep11, SPAC5D6.05 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14198 |
#14: Protein | Mass: 22374.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med20, SPAC17G8.05 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10317 |
#15: Protein | Mass: 15396.165 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: med22, srb6, SPAC29A4.07 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14010 |
-Protein , 1 types, 1 molecules F
#6: Protein | Mass: 13810.964 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: SPAC24C9.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13964 |
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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: 5.11 Å3/Da / Density % sol: 75.91 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 0.1 M MES pH 6.5, 3.2% PEG 20000, 700 mM ammonium nitrate |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.4→98.486 Å / Num. obs: 113813 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.643 % / Biso Wilson estimate: 154.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.174 / Net I/σ(I): 17.05 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.4→98.486 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 30.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 368.86 Å2 / Biso mean: 159.0468 Å2 / Biso min: 80.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→98.486 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: 30
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