[English] 日本語
Yorodumi- PDB-6o31: CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA-ACTININ-4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o31 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA-ACTININ-4 | ||||||||||||
Components | Alpha-actinin-4 | ||||||||||||
Keywords | STRUCTURAL PROTEIN / CALPONIN HOMOLOGY DOMAIN / CH DOMAIN / ACTIN- BINDING PROTEIN / ACTIN-CROSSLINKING / GLOMERULOSCLEROS SPECTRIN FAMILY / DISEASE MUTATION / NUCLEUS / PHOSPHORYLATION | ||||||||||||
Function / homology | Function and homology information positive regulation of sodium:proton antiporter activity / negative regulation of substrate adhesion-dependent cell spreading / postsynaptic actin cytoskeleton / vesicle transport along actin filament / nucleoside binding / muscle cell development / nuclear retinoic acid receptor binding / Nephrin family interactions / cortical actin cytoskeleton / retinoic acid receptor signaling pathway ...positive regulation of sodium:proton antiporter activity / negative regulation of substrate adhesion-dependent cell spreading / postsynaptic actin cytoskeleton / vesicle transport along actin filament / nucleoside binding / muscle cell development / nuclear retinoic acid receptor binding / Nephrin family interactions / cortical actin cytoskeleton / retinoic acid receptor signaling pathway / pseudopodium / peroxisome proliferator activated receptor signaling pathway / stress fiber / tumor necrosis factor-mediated signaling pathway / platelet alpha granule lumen / nuclear receptor coactivator activity / cell projection / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of non-canonical NF-kappaB signal transduction / chromatin DNA binding / Z disc / actin filament binding / integrin binding / cell junction / actin cytoskeleton / protein transport / Platelet degranulation / actin binding / actin cytoskeleton organization / regulation of apoptotic process / transcription coactivator activity / transmembrane transporter binding / positive regulation of cell migration / ribonucleoprotein complex / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||||||||
Authors | Birrane, G. / Feng, D. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: J. Am. Soc. Nephrol. / Year: 2020 Title: Phosphorylation of ACTN4 Leads to Podocyte Vulnerability and Proteinuric Glomerulosclerosis. Authors: Feng, D. / Kumar, M. / Muntel, J. / Gurley, S.B. / Birrane, G. / Stillman, I.E. / Ding, L. / Wang, M. / Ahmed, S. / Schlondorff, J. / Alper, S.L. / Ferrante, T. / Marquez, S.L. / Ng, C.F. / ...Authors: Feng, D. / Kumar, M. / Muntel, J. / Gurley, S.B. / Birrane, G. / Stillman, I.E. / Ding, L. / Wang, M. / Ahmed, S. / Schlondorff, J. / Alper, S.L. / Ferrante, T. / Marquez, S.L. / Ng, C.F. / Novak, R. / Ingber, D.E. / Steen, H. / Pollak, M.R. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6o31.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6o31.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 6o31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o31_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6o31_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 6o31_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 6o31_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/6o31 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/6o31 | HTTPS FTP |
-Related structure data
Related structure data | 6oa6C 2r0oS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26713.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN4 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4E337, UniProt: O43707*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.07 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 50mM Sodium Chloride, 5% Glycerol, 1mM EDTA, 15-18% PEG5000-MME PH range: 7.2 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2018 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→40 Å / Num. obs: 36924 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.989 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3555 / CC1/2: 0.779 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2R0O Resolution: 1.51→37.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.608 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.093 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.009 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→37.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|