[English] 日本語
![](img/lk-miru.gif)
- PDB-3uvk: Crystal structure of WDR5 in complex with the WDR5-interacting mo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3uvk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2 | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / trithorax / chromatin biology / beta-propeller / scaffolding / histone H3 / nucleus | ||||||
Function / homology | ![]() beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex ...beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / positive regulation of intracellular estrogen receptor signaling pathway / histone methyltransferase complex / regulation of tubulin deacetylation / oogenesis / 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 / heterochromatin formation / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / 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 / response to estrogen / Neddylation / HATs acetylate histones / histone binding / methylation / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of cell population proliferation / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.-F. | ||||||
![]() | ![]() Title: The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases. Authors: Zhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 144.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 111.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 468 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3uvlC ![]() 3uvmC ![]() 3uvnC ![]() 3uvoC ![]() 2h13S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34794.449 Da / Num. of mol.: 1 / Fragment: UNP residues 21-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1176.387 Da / Num. of mol.: 1 / Fragment: WDR5-interacting motif (UNP residues 5337-5347) / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: O14686, histone-lysine N-methyltransferase |
#3: Chemical | ChemComp-BTB / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
---|---|
Crystal grow | Temperature: 323 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12718 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→31.907 Å / Num. all: 55849 / Num. obs: 57766 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.041 / Net I/σ(I): 47.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.355 / % possible all: 81.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2H13 Resolution: 1.4→31.907 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.919 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.34 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.907 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.437 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|