+Open data
-Basic information
Entry | Database: PDB / ID: 4cbz | ||||||
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Title | Notch ligand, Jagged-1, contains an N-terminal C2 domain | ||||||
Components | PROTEIN JAGGED-1 | ||||||
Keywords | SIGNALING PROTEIN / SIGNALLING / GLYCOPROTEIN / EXTRACELLULAR / DEVELOPMENTAL PROTEIN / NOTCH SIGNALING PATHWAY / EGF-LIKE DOMAIN TRANSMEMBRANE / EGF-LIKE DOMAIN / DISEASE MUTATION | ||||||
Function / homology | Function and homology information endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development ...endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development / positive regulation of myeloid cell differentiation / Nephron development / cardiac right ventricle morphogenesis / inhibition of neuroepithelial cell differentiation / distal tubule development / neuroendocrine cell differentiation / aorta morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of cardiac epithelial to mesenchymal transition / NOTCH4 Activation and Transmission of Signal to the Nucleus / inner ear auditory receptor cell differentiation / T cell mediated immunity / endothelial cell differentiation / neuronal stem cell population maintenance / pulmonary valve morphogenesis / cell fate determination / negative regulation of stem cell differentiation / regulation of epithelial cell proliferation / aortic valve morphogenesis / myoblast differentiation / Notch binding / RUNX3 regulates NOTCH signaling / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / cardiac septum morphogenesis / response to muramyl dipeptide / hemopoiesis / negative regulation of neuron differentiation / RAC3 GTPase cycle / blood vessel remodeling / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / RAC1 GTPase cycle / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of cell migration / NOTCH3 Activation and Transmission of Signal to the Nucleus / adherens junction / growth factor activity / phospholipid binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nervous system development / regulation of cell population proliferation / angiogenesis / molecular adaptor activity / apical plasma membrane / calcium ion binding / structural molecule activity / positive regulation of transcription by RNA polymerase II / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chilakuri, C.R. / Sheppard, D. / Ilagan, M.X.G. / Holt, L.R. / Abbott, F. / Liang, S. / Kopan, R. / Handford, P.A. / Lea, S.M. | ||||||
Citation | Journal: Cell Rep. / Year: 2013 Title: Structural Analysis Uncovers Lipid-Binding Properties of Notch Ligands Authors: Chilakuri, C.R. / Sheppard, D. / Ilagan, M.X.G. / Holt, L.R. / Abbott, F. / Liang, S. / Kopan, R. / Handford, P.A. / Lea, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cbz.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbz.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cbz_validation.pdf.gz | 481.8 KB | Display | wwPDB validaton report |
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Full document | 4cbz_full_validation.pdf.gz | 485.2 KB | Display | |
Data in XML | 4cbz_validation.xml.gz | 21 KB | Display | |
Data in CIF | 4cbz_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbz ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbz | HTTPS FTP |
-Related structure data
Related structure data | 4cc0C 4cc1C 2vj2S C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.248, -0.594, 0.766), Vector: |
-Components
#1: Protein | Mass: 34813.750 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-335 Source method: isolated from a genetically manipulated source Details: NAG LINKAGE AT N217 IN BOTH A, B CHAINS, FUC LINKAGE AT T311 IN A CHAIN Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) / References: UniProt: P78504 #2: Sugar | #3: Sugar | ChemComp-FUC / | #4: 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: 2.96 Å3/Da / Density % sol: 58.39 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→61.12 Å / Num. obs: 22857 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 74.84 Å2 / Rmerge(I) obs: 0.12 |
-Processing
Software | Name: BUSTER / Version: 2.11.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VJ2 Resolution: 2.5→61.12 Å / Cor.coef. Fo:Fc: 0.9298 / Cor.coef. Fo:Fc free: 0.8996 / SU R Cruickshank DPI: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.438 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.283
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Displacement parameters | Biso mean: 70.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.386 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→61.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.62 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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