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- PDB-3i08: Crystal structure of the S1-cleaved Notch1 Negative Regulatory Re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i08 | ||||||
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Title | Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR) | ||||||
![]() | (Neurogenic locus notch homolog protein 1) x 2 | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gordon, W.R. / Blacklow, S.C. | ||||||
![]() | ![]() Title: Effects of S1 cleavage on the structure, surface export, and signaling activity of human Notch1 and Notch2. Authors: Gordon, W.R. / Vardar-Ulu, D. / L'Heureux, S. / Ashworth, T. / Malecki, M.J. / Sanchez-Irizarry, C. / McArthur, D.G. / Histen, G. / Mitchell, J.L. / Aster, J.C. / Blacklow, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.7 KB | Display | ![]() |
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PDB format | ![]() | 80.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3etoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 24595.336 Da / Num. of mol.: 2 / Fragment: Notch1 NRR (Residues 1446-1665) Source method: isolated from a genetically manipulated source Details: Cloned into pet15b containing an N-terminal His6 tag with a TEV protease site. Upon cleavage, a non-native Glycine remains at the N-terminus. Protein was expressed, purified from inclusion ...Details: Cloned into pet15b containing an N-terminal His6 tag with a TEV protease site. Upon cleavage, a non-native Glycine remains at the N-terminus. Protein was expressed, purified from inclusion bodies, refolded and purified as previously described. Recombinant furin incubated with the Notch1 NRR overnight, and size exclusion chromatography was used to purify the complex. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 7383.235 Da / Num. of mol.: 2 / Fragment: Notch1 NRR (Residues 1666-1734) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / | ![]() #5: Water | ChemComp-HOH / | ![]() Compound details | THE PRECURSOR STRUCTURE WAS CLEAVED IN VITRO BY FURIN PROTEASE. FURIN CLEAVES AT R1665 PRIMARILY, ...THE PRECURSOR STRUCTURE WAS CLEAVED IN VITRO BY FURIN PROTEASE. FURIN CLEAVES AT R1665 PRIMARILY, BUT A MINOR CLEAVAGE WAS OBSERVED AT R1634 VIA MASS SPECTROMET | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1M NaOAc, 2.0 M NaCl, 10% glycerol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→46 Å / Num. all: 11941 / Num. obs: 11928 / % possible obs: 94.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 74.9 Å2 / Rsym value: 0.132 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11320 / Rsym value: 0.518 / % possible all: 97.1 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: Notch1 NRR deletion (3eto) Resolution: 3.2→46.32 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.757 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
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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: 120.83 Å2 / Biso mean: 76.809 Å2 / Biso min: 38.27 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→46.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.203→3.286 Å / Total num. of bins used: 20
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