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Yorodumi- PDB-6q5y: Crystal structure of the SPOC domain of human PHF3 in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 6q5y | ||||||
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Title | Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser5 | ||||||
Components |
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Keywords | TRANSCRIPTION / SPOC domain / PHF3 / Pol II / pSer2Ser5 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: 2.85 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 | 6q5y.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q5y.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q5y_validation.pdf.gz | 480.6 KB | Display | wwPDB validaton report |
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Full document | 6q5y_full_validation.pdf.gz | 499 KB | Display | |
Data in XML | 6q5y_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 6q5y_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5y ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5y | HTTPS FTP |
-Related structure data
Related structure data | 6ic8C 6ic9C 6q2vSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 18211.150 Da / Num. of mol.: 4 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: 3.26 Å3/Da / Density % sol: 62.27 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M imidazole-MES pH 6.5, 20% glycerol and 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å | |||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2017 | |||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.85→44.53 Å / Num. obs: 21184 / % possible obs: 98.8 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.124 / Rrim(I) all: 0.183 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.432 / Num. unique obs: 3104 / Rpim(I) all: 0.819 / Rrim(I) all: 1.662 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q2V Resolution: 2.85→41.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.794 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.322 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→41.76 Å
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Refine LS restraints |
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