+Open data
-Basic information
Entry | Database: PDB / ID: 3emh | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis of WDR5-MLL interaction | ||||||
Components |
| ||||||
Keywords | GENE REGULATION / Chromatin / Histone / WD40 repeat / Nucleus / Phosphoprotein / WD repeat / Zinc-finger | ||||||
Function / homology | Function and homology information : / : / : / : / : / : / : / : / : / positive regulation of cellular response to drug ...: / : / : / : / : / : / : / : / : / positive regulation of cellular response to drug / [histone H3]-lysine4 N-trimethyltransferase / protein-cysteine methyltransferase activity / positive regulation of transporter activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / regulation of megakaryocyte differentiation / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / Set1C/COMPASS complex / MLL1/2 complex / definitive hemopoiesis / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of hematopoietic stem cell differentiation / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / positive regulation of gluconeogenesis / spleen development / lysine-acetylated histone binding / cellular response to transforming growth factor beta stimulus / methylated histone binding / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / skeletal system development / gluconeogenesis / Transcriptional regulation of granulopoiesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / circadian regulation of gene expression / PKMTs methylate histone lysines / visual learning / protein modification process / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / HATs acetylate histones / histone binding / fibroblast proliferation / protein-containing complex assembly / methylation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Song, J.J. / Kingston, R.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: WDR5 Interacts with Mixed Lineage Leukemia (MLL) Protein via the Histone H3-binding Pocket. Authors: Song, J.J. / Kingston, R.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3emh.cif.gz | 79 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3emh.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 3emh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3emh_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3emh_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 3emh_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3emh_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3emh ftp://data.pdbj.org/pub/pdb/validation_reports/em/3emh | HTTPS FTP |
-Related structure data
Related structure data | 2h13S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 34916.590 Da / Num. of mol.: 1 / Fragment: UNP residues 25-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pGEX6p_1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61964 | ||
---|---|---|---|
#2: Protein/peptide | Mass: 1503.705 Da / Num. of mol.: 1 / Fragment: UNP residues 2675-2687 / Source method: obtained synthetically Details: Synthetic peptide following the sequence position 2675-2687 of UniProt entry Q59FF2 (Q59FF2_HUMAN) References: UniProt: Q59FF2, UniProt: Q03164*PLUS | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mM HEPES, 15-20% PEG 3350, 60mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2008 |
Radiation | Monochromator: 100 um / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→50 Å / Num. all: 64701 / Num. obs: 65115 / % possible obs: 99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 1.37→1.41 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 90.3 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2H13 Resolution: 1.37→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→50 Å
| ||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||
LS refinement shell | Resolution: 1.37→1.42 Å /
|