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Yorodumi- PDB-1cz8: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH AN AFFINITY MA... -
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-Basic information
Entry | Database: PDB / ID: 1cz8 | ||||||
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Title | VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH AN AFFINITY MATURED ANTIBODY | ||||||
Components |
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Keywords | IMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / CYSTINE KNOT / FAB FRAGMENT | ||||||
Function / homology | Function and homology information basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis ...basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / motor neuron migration / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / eye photoreceptor cell development / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / camera-type eye morphogenesis / positive regulation of epithelial tube formation / negative regulation of cell-cell adhesion mediated by cadherin / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / positive regulation of vascular permeability / dopaminergic neuron differentiation / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / activation of protein kinase activity / chemoattractant activity / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / extracellular matrix / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / secretory granule / kidney development / cytokine activity / positive regulation of epithelial cell proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Chen, Y. / Wiesmann, C. / Fuh, G. / Li, B. / Christinger, H.W. / McKay, P. / de Vos, A.M. / Lowman, H.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen. Authors: Chen, Y. / Wiesmann, C. / Fuh, G. / Li, B. / Christinger, H.W. / McKay, P. / de Vos, A.M. / Lowman, H.B. #1: Journal: Structure / Year: 1998 Title: VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface. Authors: Muller, Y.A. / Chen, Y. / Christinger, H.W. / Li, B. / Cunningham, B.C. / Lowman, H.B. / M de Vos, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cz8.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cz8.ent.gz | 180.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1cz8 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1cz8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10999.722 Da / Num. of mol.: 2 / Fragment: RECEPTOR BINDING FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Production host: Escherichia coli (E. coli) / References: UniProt: P15692 #2: Antibody | Mass: 23453.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MUTATED FORM OF A HUMANIZED MURINE ANTIBODY LIGHT CHAIN Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 24979.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MUTATED FORM OF A HUMANIZED MURINE ANTIBODY HEAVY CHAIN Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #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: 3.53 Å3/Da / Density % sol: 65.11 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, ISOPROPANOL, AMMONIUM SULFATE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC / Detector: CCD / Date: Jan 28, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 61742 / Num. obs: 61742 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 209257 |
Reflection shell | *PLUS % possible obs: 96.7 % / Num. unique obs: 8900 / Num. measured obs: 22278 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Resolution: 2.4→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 50.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR / Version: 98.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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