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Open data
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Basic information
Entry | Database: PDB / ID: 5x4z | ||||||
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Title | RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) | ||||||
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![]() | TRANSFERASE / transcription / RNA polymerase | ||||||
Function / homology | ![]() 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 / transcription initiation at RNA polymerase III promoter ...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 / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / pericentric heterochromatin / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / translation initiation factor binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ehara, H. / Umehara, T. / Sekine, S. / Yokoyama, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 751.4 KB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 338.6 KB | Display | |
Data in CIF | ![]() | 446 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() 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) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R009 |
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-Protein / Non-polymers , 2 types, 18 molecules LX![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#12: Protein | Mass: 7972.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QWA8 #13: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]()
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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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