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Yorodumi- PDB-6ic9: Crystal structure of the SPOC domain of human PHF3 in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 6ic9 | ||||||
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Title | Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser7 | ||||||
Components |
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Keywords | TRANSCRIPTION / SPOC domain / PHF3 / pSER2 peptide | ||||||
Function / homology | Function and homology information microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Inhibition of DNA recombination at telomere / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription termination / kinase binding / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.748 Å | ||||||
Authors | Grishkovskaya, I. / Djinovic-Carugo, K. / Slade, D. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Kaufmann, T. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Ebenwaldner, C. / Sebesta, M. / Beltzung, E. ...Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Kaufmann, T. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Ebenwaldner, C. / Sebesta, M. / Beltzung, E. / Mechtler, K. / Lin, G. / Vlasova, A. / Leeb, M. / Pavri, R. / Stark, A. / Akalin, A. / Stefl, R. / Bernecky, C. / Djinovic-Carugo, K. / Slade, D. #1: Journal: Biorxiv / Year: 2020 Title: PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Beltzung, E. / Mechtler, K. / Lin, G. / Vlasova, A. / Leeb, ...Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Beltzung, E. / Mechtler, K. / Lin, G. / Vlasova, A. / Leeb, M. / Pavri, R. / Stark, A. / Akalin, A. / Stefl, R. / Bernecky, C. / Djinovic-Carugo, K. / Slade, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ic9.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ic9.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ic9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ic9_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 6ic9_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 6ic9_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 6ic9_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/6ic9 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6ic9 | 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
#1: Protein | Mass: 18211.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHF3, KIAA0244 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92576 #2: Protein/peptide | Mass: 1777.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24928*PLUS #3: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 10% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.748→49.1 Å / Num. obs: 39627 / % possible obs: 99.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 35.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.753 / Num. unique obs: 1968 / CC1/2: 0.223 / Rpim(I) all: 1.476 / Rrim(I) all: 3.143 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.748→49.1 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.77 Å2 / Biso mean: 40.8204 Å2 / Biso min: 21.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.748→49.1 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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