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- PDB-6oi1: Crystal structure of human WDR5 in complex with monomethyl L-arginine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oi1 | ||||||
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Title | Crystal structure of human WDR5 in complex with monomethyl L-arginine | ||||||
![]() | WD repeat-containing protein 5 | ||||||
![]() | GENE REGULATION / Methylation / Epigenetics / Post-translational modification / Chromatin / Methylarginine | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lorton, B.M. / Harijan, R.K. / Burgos, E. / Bonanno, J.B. / Almo, S.C. / Shechter, D. | ||||||
![]() | ![]() Title: A Binary Arginine Methylation Switch on Histone H3 Arginine 2 Regulates Its Interaction with WDR5. Authors: Lorton, B.M. / Harijan, R.K. / Burgos, E.S. / Bonanno, J.B. / Almo, S.C. / Shechter, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.5 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.3 KB | Display | ![]() |
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Full document | ![]() | 457.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ofzC ![]() 6oi0C ![]() 6oi2C ![]() 6oi3C ![]() 2h14S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34390.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-NMM / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 100mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM monomethyl L-arginine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2018 / Details: KB mirrors |
Radiation | Monochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→59.06 Å / Num. obs: 33408 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.03 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1685 / Rpim(I) all: 0.37 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H14 Resolution: 1.68→59.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.694 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.785 Å2
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Refinement step | Cycle: 1 / Resolution: 1.68→59.06 Å
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Refine LS restraints |
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