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Yorodumi- PDB-6ded: Crystal structure of the C-terminal ARM domain of Homo sapiens SP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ded | ||||||
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Title | Crystal structure of the C-terminal ARM domain of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 351-722 | ||||||
Components | NCK-interacting protein with SH3 domain | ||||||
Keywords | ENDOCYTOSIS / inactive form / N-terminally truncated SPIN90 / 6 and 2-3 armadillo repeats / unable to activate Arp2-3 complex | ||||||
Function / homology | Function and homology information Arp2/3 complex binding / intermediate filament / RHO GTPases Activate WASPs and WAVEs / cytoskeleton organization / cytoskeletal protein binding / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / positive regulation of neuron projection development / SH3 domain binding / endocytosis ...Arp2/3 complex binding / intermediate filament / RHO GTPases Activate WASPs and WAVEs / cytoskeleton organization / cytoskeletal protein binding / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / positive regulation of neuron projection development / SH3 domain binding / endocytosis / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å | ||||||
Authors | Nolen, B.J. / Luan, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: EMBO J. / Year: 2018 Title: Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex. Authors: Luan, Q. / Liu, S.L. / Helgeson, L.A. / Nolen, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ded.cif.gz | 288 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ded.ent.gz | 233.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ded.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ded_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 6ded_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 6ded_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 6ded_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/6ded ftp://data.pdbj.org/pub/pdb/validation_reports/de/6ded | HTTPS FTP |
-Related 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: 42291.148 Da / Num. of mol.: 2 / Fragment: UNP residues 350-722 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCKIPSD, AF3P21, SPIN90 / Plasmid: pGv67 Details (production host): N-terminal GST-fusion with TEV cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9NZQ3 #2: Water | ChemComp-HOH / | |
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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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM Tris, pH 7.5, 700 mM sodium potassium tartrate Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9797423 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2016 / Details: Sagitally focusing 2nd crystal |
Radiation | Monochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797423 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 53032 / % possible obs: 99.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 47.5 Å2 / Rpim(I) all: 0.087 / Rrim(I) all: 0.147 / Rsym value: 0.131 / Χ2: 2.374 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2657 / CC1/2: 0.302 / Χ2: 1.356 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD model Resolution: 2.204→35.699 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.204→35.699 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.2927 Å / Origin y: 7.3402 Å / Origin z: -23.7301 Å
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Refinement TLS group | Selection details: all |