+Open data
-Basic information
Entry | Database: PDB / ID: 5xon | ||||||
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Title | RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS | ||||||
Components |
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Keywords | TRANSCRIPTION/RNA / transcription / complex / TRANSCRIPTION-RNA complex | ||||||
Function / homology | Function and homology information : / regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / transcription elongation-coupled chromatin remodeling ...: / regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / transcription elongation-coupled chromatin remodeling / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA polymerase III activity / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / chromosome, centromeric region / RNA polymerase II activity / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / translation elongation factor activity / pericentric heterochromatin / RNA polymerase II, core complex / translation initiation factor binding / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription elongation by RNA polymerase II / P-body / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Komagataella phaffii (fungus) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å | ||||||
Authors | Ehara, H. / Yokoyama, T. / Shigematsu, 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5xon.cif.gz | 992.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xon.ent.gz | 774.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xon ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xon | HTTPS FTP |
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-Related structure data
Related structure data | 6747MC 5xogC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / References: UniProt: C4QY79 |
-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 ... , 4 types, 4 molecules EFHJ
#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 |
-Protein , 4 types, 4 molecules LUVW
#12: Protein | Mass: 7862.048 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: C4QWA8 |
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#16: Protein | Mass: 21694.734 Da / Num. of mol.: 1 / Fragment: UNP residues 99-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-2_0135 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R2R6 |
#17: Protein | Mass: 12039.614 Da / Num. of mol.: 1 / Fragment: UNP residues 8-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6 |
#18: Protein | Mass: 68283.984 Da / Num. of mol.: 1 / Fragment: UNP residues 206-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R370 |
-RNA chain , 1 types, 1 molecules P
#13: RNA chain | Mass: 9492.561 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: 14659.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: DNA chain | Mass: 14917.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 11 molecules
#19: Chemical | ChemComp-ZN / #20: Chemical | ChemComp-MG / | |
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-Details
Sequence details | FOR ENTITY 9 AND 12, THE SEQUENCE REFERENCE IN UNIPROT (C4QY79 AND C4QWA8) CONTAIN ERRORS. AND ...FOR ENTITY 9 AND 12, THE SEQUENCE REFERENCE IN UNIPROT (C4QY79 AND C4QWA8) CONTAIN ERRORS. AND AUTHOR CONFIRMED THE SEQUENCES IN THIS ENTRY ARE CORRECT. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3607 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 682749 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: Model fitting was done with Chimera and Coot. Well-ordered regions were also refined with phenix.real_space_refine. |