+Open data
-Basic information
Entry | Database: PDB / ID: 2gnq | ||||||
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Title | Structure of wdr5 | ||||||
Components | WD-repeat protein 5WD40 repeat | ||||||
Keywords | TRANSCRIPTION / h3k4me2 binding protein / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Min, J. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. ...Min, J. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structural basis for molecular recognition and presentation of histone H3 By WDR5. Authors: Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Bochkarev, A. / Plotnikov, A.N. / Arrowsmith, C.H. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gnq.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gnq.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/2gnq ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gnq | HTTPS FTP |
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-Related structure data
Related structure data | 2h9lC 2h9mC 2h9nC 2h9pC 2o9kC 1vyhS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36779.566 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: Chemical | ChemComp-CL / |
#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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20%peg5k mme, bis-tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 8, 2006 |
Radiation | Monochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→62.14 Å / Num. all: 30580 / Num. obs: 30580 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 62.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VYH Resolution: 1.8→62.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.853 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.759 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→62.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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