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Yorodumi- PDB-5wfn: Revised model of leiomodin 2-mediated actin regulation (alternate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wfn | |||||||||
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Title | Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT) | |||||||||
Components |
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Keywords | MOTOR PROTEIN / actin regulation / leiomodin / filament nucleation | |||||||||
Function / homology | Function and homology information Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / pointed-end actin filament capping / MAP2K and MAPK activation ...Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / pointed-end actin filament capping / MAP2K and MAPK activation / Platelet degranulation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / DNA Damage Recognition in GG-NER / Clathrin-mediated endocytosis / myofibril assembly / UCH proteinases / sperm individualization / actin nucleation / maintenance of protein location in cell / brahma complex / Ino80 complex / tube formation / M band / sarcomere organization / myofibril / positive regulation of actin filament polymerization / tropomyosin binding / striated muscle thin filament / mitotic cytokinesis / actin monomer binding / muscle contraction / actin filament polymerization / sarcomere / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin binding / chromatin remodeling / cytoskeleton / hydrolase activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | |||||||||
Authors | Yurtsever, Z. / Eck, M.J. / Dominguez, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 Title: Mechanisms of leiomodin 2-mediated regulation of actin filament in muscle cells. Authors: Chen, X. / Ni, F. / Kondrashkina, E. / Ma, J. / Wang, Q. | |||||||||
History |
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Remark 0 | This entry reflects an alternative modeling of the original data in 4RWT, determined by X.Chen, F. ...This entry reflects an alternative modeling of the original data in 4RWT, determined by X.Chen, F.Ni, E.Kondrashkina, J.Ma, Q.Wang. | |||||||||
Remark 200 | SEE THE ORIGINAL DATA, ENTRY 4RWT | |||||||||
Remark 280 | SEE THE ORIGINAL DATA, ENTRY 4RWT |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wfn.cif.gz | 646.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wfn.ent.gz | 531.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wfn_validation.pdf.gz | 987 KB | Display | wwPDB validaton report |
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Full document | 5wfn_full_validation.pdf.gz | 996.7 KB | Display | |
Data in XML | 5wfn_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 5wfn_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/5wfn ftp://data.pdbj.org/pub/pdb/validation_reports/wf/5wfn | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42886.793 Da / Num. of mol.: 2 / Mutation: K291E, P322K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10987 #2: Protein | Mass: 56753.699 Da / Num. of mol.: 2 Mutation: del(97-128), del(421-440), K426G, K427S, K428G, K429S, K431G, K432S, K434G, K435S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LMOD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P5Q4 #3: Chemical | #4: Chemical | |
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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: 1.64 Å3/Da / Density % sol: 24.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG3350, 0.2 M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2014 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→51.07 Å / Num. obs: 25186 / % possible obs: 97.5 % |
Reflection shell | Highest resolution: 2.98 Å |
-Processing
Software | Name: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3→44.245 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 25.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→44.245 Å
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Refine LS restraints |
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LS refinement shell |
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