+Open data
-Basic information
Entry | Database: PDB / ID: 3ur4 | ||||||
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Title | Crystal structure of human WD repeat domain 5 with compound | ||||||
Components | WD repeat-containing protein 5 | ||||||
Keywords | TRANSCRIPTION/INHIBITOR / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION / WD REPEAT DOMAIN 5 / WDR5 / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / 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 / 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 / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 | Dong, A. / Dombrovski, L. / Senisterra, G. / Wernimont, A. / Wasney, G.A. / Allali Hassani, A. / Nguyen, K.T. / Smil, D. / Bolshan, Y. / Hajian, T. ...Dong, A. / Dombrovski, L. / Senisterra, G. / Wernimont, A. / Wasney, G.A. / Allali Hassani, A. / Nguyen, K.T. / Smil, D. / Bolshan, Y. / Hajian, T. / Poda, G. / Chau, I. / Al-Awar, R. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P. / Schapira, M. / Vedadi, M. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Biochem. J. / Year: 2013 Title: Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5. Authors: Senisterra, G. / Wu, H. / Allali-Hassani, A. / Wasney, G.A. / Barsyte-Lovejoy, D. / Dombrovski, L. / Dong, A. / Nguyen, K.T. / Smil, D. / Bolshan, Y. / Hajian, T. / He, H. / Seitova, A. / ...Authors: Senisterra, G. / Wu, H. / Allali-Hassani, A. / Wasney, G.A. / Barsyte-Lovejoy, D. / Dombrovski, L. / Dong, A. / Nguyen, K.T. / Smil, D. / Bolshan, Y. / Hajian, T. / He, H. / Seitova, A. / Chau, I. / Li, F. / Poda, G. / Couture, J.F. / Brown, P.J. / Al-Awar, R. / Schapira, M. / Arrowsmith, C.H. / Vedadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ur4.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ur4.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ur4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ur4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3ur4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ur4_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 3ur4_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/3ur4 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/3ur4 | HTTPS FTP |
-Related structure data
Related structure data | 3smrSC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34289.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2RpRARE / References: UniProt: P61964 |
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-Non-polymers , 6 types, 765 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-UNX / #7: 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: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 22% PEG 3350,0.1M A.S. ,0.1M Bis Tris pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 2, 2011 / Details: VariMax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 57305 / Num. obs: 57305 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2303 / Rsym value: 0.165 / % possible all: 79.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SMR Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.685 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.123 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.369 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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