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Yorodumi- PDB-5xog: RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1 -
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-Basic information
Entry | Database: PDB / ID: 5xog | ||||||
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Title | RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1 | ||||||
Components |
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Keywords | TRANSCRIPTION / complex | ||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DSIF complex / 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 ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DSIF complex / 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 / regulation of DNA-templated transcription elongation / 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 / mRNA binding / nucleotide binding / regulation of transcription by RNA polymerase II / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Komagataella pastoris (fungus) Komagataella phaffii (fungus) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ehara, H. / Shirouzu, M. / Sekine, S. | ||||||
Citation | Journal: Science / Year: 2017 Title: Structure of the complete elongation complex of RNA polymerase II with basal factors. Authors: Haruhiko Ehara / Takeshi Yokoyama / Hideki Shigematsu / Shigeyuki Yokoyama / Mikako Shirouzu / Shun-Ichi Sekine / Abstract: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we ...In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xog.cif.gz | 877.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xog.ent.gz | 688.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xog_validation.pdf.gz | 898.5 KB | Display | wwPDB validaton report |
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Full document | 5xog_full_validation.pdf.gz | 944.8 KB | Display | |
Data in XML | 5xog_validation.xml.gz | 133.7 KB | Display | |
Data in CIF | 5xog_validation.cif.gz | 186.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xog ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xog | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI
#1: Protein | Mass: 194107.422 Da / Num. of mol.: 1 / 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 |
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#2: Protein | Mass: 139746.094 Da / Num. of mol.: 1 / 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.: 1 / 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 |
-RNA polymerase II ... , 4 types, 4 molecules CDGK
#3: Protein | Mass: 34216.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2 |
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#4: Protein | Mass: 20622.980 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5 |
-RNA polymerase subunit ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8 |
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#6: Protein | Mass: 17803.588 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / Source method: isolated from a natural source Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4R009 |
#12: Protein | Mass: 7862.048 Da / Num. of mol.: 1 / 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: F2QMI1 |
-RNA chain , 1 types, 1 molecules P
#13: RNA chain | Mass: 5384.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-DNA chain , 2 types, 2 molecules TN
#14: DNA chain | Mass: 11909.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: DNA chain | Mass: 9315.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 2 types, 2 molecules MW
#16: Protein | Mass: 9414.886 Da / Num. of mol.: 1 / Fragment: UNP residues 1-82 / Mutation: N53G, L54Q, S55R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: ELF1, ATY40_BA7504229 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2JER8 |
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#17: Protein | Mass: 9201.514 Da / Num. of mol.: 1 / Fragment: UNP residues 736-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1 Gene: SPT5, PP7435_Chr3-0027 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QUC3 |
-Non-polymers , 3 types, 11 molecules
#18: Chemical | ChemComp-ZN / #19: Chemical | ChemComp-MG / | #20: Chemical | ChemComp-APC / | |
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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: 3 Å3/Da / Density % sol: 59.06 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→49.552 Å / Num. obs: 134084 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.733 % / Biso Wilson estimate: 84.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.119 / Χ2: 1.026 / Net I/σ(I): 15.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.552 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.98 / Phase error: 21.98 Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 348.62 Å2 / Biso mean: 92.111 Å2 / Biso min: 23.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→49.552 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: 21 / % reflection obs: 100 %
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