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Yorodumi- PDB-8wxu: Structure of WDR5 in complex with WIN motif containing MBD3C C44S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wxu | ||||||
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Title | Structure of WDR5 in complex with WIN motif containing MBD3C C44S/R45E/V46G | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / WDR5 / MBD3C / WIN motif / chromatin | ||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Xu, L. / Yang, Y. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode. Authors: Yang, Y. / Xu, L. / Zhang, S. / Yao, L. / Ding, Y. / Li, W. / Chen, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wxu.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wxu.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 8wxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wxu_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
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Full document | 8wxu_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 8wxu_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 8wxu_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/8wxu ftp://data.pdbj.org/pub/pdb/validation_reports/wx/8wxu | HTTPS FTP |
-Related structure data
Related structure data | 8wxqC 8wxrC 8wxtC 8wxvC 8wxxC C: citing same article (ref.) |
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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: 34646.309 Da / Num. of mol.: 1 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 |
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#2: Protein/peptide | Mass: 1164.207 Da / Num. of mol.: 1 / Mutation: C44S,R45E,V46G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium chloride, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→50 Å / Num. obs: 12679 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.15 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.513 / Num. unique obs: 640 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→39.9 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→39.9 Å
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Refine LS restraints |
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LS refinement shell |
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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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