+
Open data
-
Basic information
Entry | Database: PDB / ID: 3wa0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of merlin complexed with DCAF1/VprBP | ||||||
![]() |
| ||||||
![]() | CELL ADHESION / merlin FERM domain | ||||||
Function / homology | ![]() regulation of hippo signaling / RHO GTPases activate PAKs / histone H2AT120 kinase activity / regulation of organelle assembly / cell competition in a multicellular organism / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein ...regulation of hippo signaling / RHO GTPases activate PAKs / histone H2AT120 kinase activity / regulation of organelle assembly / cell competition in a multicellular organism / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / Regulation of actin dynamics for phagocytic cup formation / ectoderm development / positive regulation of protein localization to early endosome / lens fiber cell differentiation / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / V(D)J recombination / cell-cell junction organization / Cul4-RING E3 ubiquitin ligase complex / regulation of protein localization to nucleus / negative regulation of MAPK cascade / cortical actin cytoskeleton / negative regulation of cell-cell adhesion / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / ubiquitin-like ligase-substrate adaptor activity / regulation of neurogenesis / positive regulation of stress fiber assembly / ruffle / B cell differentiation / post-translational protein modification / filopodium / hippocampus development / nuclear estrogen receptor binding / positive regulation of cell differentiation / adherens junction / regulation of protein stability / brain development / negative regulation of cell growth / fibrillar center / beta-catenin binding / positive regulation of protein catabolic process / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / integrin binding / lamellipodium / apical part of cell / actin binding / regulation of cell population proliferation / regulation of cell shape / cell body / actin cytoskeleton organization / regulation of apoptotic process / early endosome / cytoskeleton / non-specific serine/threonine protein kinase / regulation of cell cycle / protein ubiquitination / neuron projection / negative regulation of cell population proliferation / protein domain specific binding / phosphorylation / protein serine kinase activity / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mori, T. / Gotoh, S. / Shirakawa, M. / Hakoshima, T. | ||||||
![]() | ![]() Title: Structural basis of DDB1-and-Cullin 4-associated Factor 1 (DCAF1) recognition by merlin/NF2 and its implication in tumorigenesis by CD44-mediated inhibition of merlin suppression of DCAF1 function. Authors: Mori, T. / Gotoh, S. / Shirakawa, M. / Hakoshima, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 380.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 311.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 536.2 KB | Display | |
Data in XML | ![]() | 67.3 KB | Display | |
Data in CIF | ![]() | 93.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1isnS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 35517.992 Da / Num. of mol.: 6 / Fragment: UNP residues 19-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 10486.212 Da / Num. of mol.: 2 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Protein/peptide , 3 types, 3 molecules IJK
#3: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#4: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein/peptide | Mass: 528.644 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 1 types, 543 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
---|
-Details
Sequence details | SEQUENCE OF CHAIN G,H,I,J,K CORRESPONDS TO ISOFORM 2, Q9Y4B6-2. THE DEPOSITORS BELIEVE THAT CHAIN ...SEQUENCE OF CHAIN G,H,I,J,K CORRESPOND |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jun 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20.07 Å / Num. obs: 120906 / % possible obs: 99.7 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ISN Resolution: 2.31→20.07 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 143.79 Å2 / Biso mean: 60.9055 Å2 / Biso min: 21.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→20.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.31→2.369 Å / Total num. of bins used: 20
|