+Open data
-Basic information
Entry | Database: PDB / ID: 4cc1 | ||||||
---|---|---|---|---|---|---|---|
Title | Notch ligand, Jagged-1, contains an N-terminal C2 domain | ||||||
Components | PROTEIN JAGGED-1 | ||||||
Keywords | SIGNALING PROTEIN / GLYCOPROTEIN / EXTRACELLULAR / DEVELOPMENTAL PROTEIN / NOTCH SIGNALING PATHWAY / EGF / DSL / LIPID / NOTCH / MEMBRANE / PROTEIN-BINDING / 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: 2.84 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cc1.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cc1.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cc1_validation.pdf.gz | 492.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cc1_full_validation.pdf.gz | 496.2 KB | Display | |
Data in XML | 4cc1_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 4cc1_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4cc1 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4cc1 | HTTPS FTP |
-Related structure data
Related structure data | 4cbzC 4cc0C 2vj2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.3, -0.597, 0.744), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#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 |
---|
-Sugars , 2 types, 3 molecules
#2: Sugar | #3: Sugar | ChemComp-FUC / | |
---|
-Non-polymers , 4 types, 16 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.47 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→60.38 Å / Num. obs: 17793 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.45 % / Biso Wilson estimate: 91.13 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.3 |
-Processing
Software | Name: BUSTER / Version: 2.11.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VJ2 Resolution: 2.84→60.38 Å / Cor.coef. Fo:Fc: 0.9121 / Cor.coef. Fo:Fc free: 0.8577 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.354
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.42 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→60.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.84→3.01 Å / Total num. of bins used: 9
|