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Yorodumi- PDB-7zdd: Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zdd | ||||||
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Title | Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K10ac histone peptide. | ||||||
Components |
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Keywords | TRANSCRIPTION / E3 ubiquitin-protein ligase / acetylation | ||||||
Function / homology | Function and homology information co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / nucleosome / protein ubiquitination ...co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / nucleosome / protein ubiquitination / protein heterodimerization activity / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.625 Å | ||||||
Authors | Caria, S. / Duclos, S. / Crespillo, S. / Errey, J. / Barker, J.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: Identification of Histone Peptide Binding Specificity and Small-Molecule Ligands for the TRIM33 alpha and TRIM33 beta Bromodomains. Authors: Sekirnik, A.R. / Reynolds, J.K. / See, L. / Bluck, J.P. / Scorah, A.R. / Tallant, C. / Lee, B. / Leszczynska, K.B. / Grimley, R.L. / Storer, R.I. / Malattia, M. / Crespillo, S. / Caria, S. / ...Authors: Sekirnik, A.R. / Reynolds, J.K. / See, L. / Bluck, J.P. / Scorah, A.R. / Tallant, C. / Lee, B. / Leszczynska, K.B. / Grimley, R.L. / Storer, R.I. / Malattia, M. / Crespillo, S. / Caria, S. / Duclos, S. / Hammond, E.M. / Knapp, S. / Morris, G.M. / Duarte, F. / Biggin, P.C. / Conway, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zdd.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zdd.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 7zdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/7zdd ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zdd | HTTPS FTP |
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-Related structure data
Related structure data | 5mr8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22274.467 Da / Num. of mol.: 1 / Fragment: UNP residues 882-1073 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9UPN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||||
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#2: Protein/peptide | Mass: 1233.463 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Peptide contains an extra lysine on the C-terminus when compared with the wild-type [ARTKQTARK(ac)] Source: (synth.) Homo sapiens (human) / References: UniProt: P0DPK5 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density meas: 1 Mg/m3 / Density % sol: 45.09 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% w/v PEG 6000 PH range: 5 |
-Data collection
Diffraction | Mean temperature: 197 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2021 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.625→37.385 Å / Num. obs: 16564 / % possible obs: 92.2 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.625→1.776 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.184 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 829 / CC1/2: 0.595 / Rpim(I) all: 0.462 / % possible all: 57.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MR8 Resolution: 1.625→37.38 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.151
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Displacement parameters | Biso mean: 24.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.625→37.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.625→1.72 Å
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