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Yorodumi- PDB-3uvn: Crystal structure of WDR5 in complex with the WDR5-interacting mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uvn | ||||||
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Title | Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1A | ||||||
Components |
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Keywords | TRANSCRIPTION / trithorax / chromatin biology / beta-propeller / scaffolding / histone H3 / nucleus | ||||||
Function / homology | Function and homology information regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity ...regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of hematopoietic stem cell differentiation / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / brain development / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / beta-catenin binding / Neddylation / HATs acetylate histones / histone binding / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of cell cycle / nuclear speck / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å | ||||||
Authors | Zhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.-F. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases. Authors: Zhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uvn.cif.gz | 251 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uvn.ent.gz | 201.5 KB | Display | PDB format |
PDBx/mmJSON format | 3uvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uvn_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 3uvn_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 3uvn_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 3uvn_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/3uvn ftp://data.pdbj.org/pub/pdb/validation_reports/uv/3uvn | HTTPS FTP |
-Related structure data
Related structure data | 3uvkC 3uvlC 3uvmC 3uvoC 2h13S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 34794.449 Da / Num. of mol.: 2 / Fragment: UNP residues 21-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964 #2: Protein/peptide | Mass: 1200.280 Da / Num. of mol.: 2 / Fragment: WDR5-interacting motif (UNP residues 1492-1502) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: O15047, histone-lysine N-methyltransferase #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: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG3350, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12718 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12718 Å / Relative weight: 1 |
Reflection | Resolution: 1.792→42.401 Å / Num. all: 69653 / Num. obs: 68329 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 23.36 Å2 / Rsym value: 0.09 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.792→2.2 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.3 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H13 Resolution: 1.792→42.401 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9127 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→42.401 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.792→1.84 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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