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Yorodumi- PDB-5bo1: Crystal structure of a human Jag1 fragment in complex with an ant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bo1 | ||||||
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Title | Crystal structure of a human Jag1 fragment in complex with an anti-Jag1 Fab | ||||||
Components |
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Keywords | Signaling protein/Immune system / Jag / Notch / antagonist / Signaling protein-Immune system complex | ||||||
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 / 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 / T cell mediated immunity / positive regulation of cardiac epithelial to mesenchymal transition / NOTCH4 Activation and Transmission of Signal to the Nucleus / inner ear auditory receptor cell differentiation / 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 / Notch binding / myoblast differentiation / RUNX3 regulates NOTCH signaling / negative regulation of fat cell differentiation / negative regulation of cell-matrix adhesion / positive regulation of Notch signaling pathway / negative regulation of cell-cell adhesion / cardiac septum morphogenesis / response to muramyl dipeptide / hemopoiesis / negative regulation of neuron differentiation / RAC3 GTPase cycle / positive regulation of osteoblast differentiation / blood vessel remodeling / Notch signaling pathway / keratinocyte differentiation / 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 / phospholipid binding / growth factor activity / 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: 2.56 Å | ||||||
Authors | Payandeh, J. / de Leon-Boenig, G. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Therapeutic antibodies reveal Notch control of transdifferentiation in the adult lung. Authors: Lafkas, D. / Shelton, A. / Chiu, C. / de Leon Boenig, G. / Chen, Y. / Stawicki, S.S. / Siltanen, C. / Reichelt, M. / Zhou, M. / Wu, X. / Eastham-Anderson, J. / Moore, H. / Roose-Girma, M. / ...Authors: Lafkas, D. / Shelton, A. / Chiu, C. / de Leon Boenig, G. / Chen, Y. / Stawicki, S.S. / Siltanen, C. / Reichelt, M. / Zhou, M. / Wu, X. / Eastham-Anderson, J. / Moore, H. / Roose-Girma, M. / Chinn, Y. / Hang, J.Q. / Warming, S. / Egen, J. / Lee, W.P. / Austin, C. / Wu, Y. / Payandeh, J. / Lowe, J.B. / Siebel, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bo1.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bo1.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 5bo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/5bo1 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5bo1 | HTTPS FTP |
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-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: 16711.746 Da / Num. of mol.: 2 / Fragment: UNP residues 186-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAG1, JAGL1 / Plasmid: pAcGP67A / Details (production host): modified pAcGP67A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P78504 #2: Antibody | Mass: 22990.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: engineered antibody / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 23341.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: engineered antibody / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) #4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 100 mM CHES pH 9.5, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→71.79 Å / Num. obs: 41207 / % possible obs: 96.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 59.89 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.56→2.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.8 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VJ2, 2R0L Resolution: 2.56→71.79 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.86 / SU R Cruickshank DPI: 0.72 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.668 / SU Rfree Blow DPI: 0.303 / SU Rfree Cruickshank DPI: 0.31
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Displacement parameters | Biso mean: 41.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→71.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.63 Å / Total num. of bins used: 20
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