+Open data
-Basic information
Entry | Database: PDB / ID: 5x4z | ||||||
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Title | RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) | ||||||
Components |
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Keywords | TRANSFERASE / transcription / RNA polymerase | ||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / pericentric heterochromatin / translation initiation factor binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-dependent RNA polymerase activity / nucleotide binding / nucleolus / DNA binding / RNA binding / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Komagataella phaffii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.8 Å | ||||||
Authors | Ehara, H. / Umehara, T. / Sekine, S. / Yokoyama, S. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Crystal structure of RNA polymerase II from Komagataella pastoris Authors: Ehara, H. / Umehara, T. / Sekine, S.I. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x4z.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5x4z.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5x4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x4z_validation.pdf.gz | 751.4 KB | Display | wwPDB validaton report |
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Full document | 5x4z_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5x4z_validation.xml.gz | 338.6 KB | Display | |
Data in CIF | 5x4z_validation.cif.gz | 446 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/5x4z ftp://data.pdbj.org/pub/pdb/validation_reports/x4/5x4z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase ... , 3 types, 6 molecules AMBNIU
#1: Protein | Mass: 194107.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase #2: Protein | Mass: 139746.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase #9: Protein | Mass: 13612.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus) Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1 References: UniProt: F2QPE6 |
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-RNA polymerase II ... , 4 types, 8 molecules CODPGSKW
#3: Protein | Mass: 34216.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2 #4: Protein | Mass: 20622.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9 #7: Protein | Mass: 18802.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1 #11: Protein | Mass: 13832.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5 |
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-RNA polymerase subunit ... , 4 types, 8 molecules EQFRHTJV
#5: Protein | Mass: 24962.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8 #6: Protein | Mass: 17803.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1 #8: Protein | Mass: 16249.220 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R273 #10: Protein | Mass: 8554.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R009 |
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-Protein / Non-polymers , 2 types, 18 molecules LX
#12: Protein | Mass: 7972.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4QWA8 #13: Chemical | ChemComp-ZN / |
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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: 2.99 Å3/Da / Density % sol: 58.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium citrate, 8% PGA-LM, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 5, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 7.8→50 Å / Num. obs: 13973 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 275.68 Å2 / Rmerge(I) obs: 0.378 / Rpim(I) all: 0.27 / Rrim(I) all: 0.407 / Χ2: 1.254 / Net I/σ(I): 2.2 / Num. measured all: 51715 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.8→49.82 Å / SU ML: 1.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.83 / Stereochemistry target values: ML
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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 max: 276.92 Å2 / Biso mean: 186.529 Å2 / Biso min: 112.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 7.8→49.82 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: 10
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