+Open data
-Basic information
Entry | Database: PDB / ID: 1rv6 | ||||||
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Title | Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1 | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR/RECEPTOR / PlGF / VEGF family / cystine knot / growth factor / ligand-receptor complex / specificity / HORMONE-GROWTH FACTOR-RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / induction of positive chemotaxis / sprouting angiogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / growth factor binding / monocyte chemotaxis / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / : / positive regulation of endothelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / growth factor activity / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / cell migration / actin cytoskeleton / cell-cell signaling / heparin binding / angiogenesis / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / response to hypoxia / endosome / positive regulation of cell migration / positive regulation of protein phosphorylation / focal adhesion / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Christinger, H.W. / Fuh, G. / de Vos, A.M. / Wiesmann, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The crystal structure of placental growth factor in complex with domain 2 of vascular endothelial growth factor receptor-1. Authors: Christinger, H.W. / Fuh, G. / de Vos, A.M. / Wiesmann, C. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Crystal structure at 1.7 A resolution of VEGF in complex with domain 2 of the Flt-1 receptor Authors: Wiesmann, C. / Fuh, G. / Christinger, C.H. / Eigenbrot, C. / Wells, J.A. / de Vos, A.M. #2: Journal: J.Biol.Chem. / Year: 2001 Title: The crystal structure of human placenta growth factor-1 (PlGF-1), an angiogenic protein, at 2.0 A resolution. Authors: Iyer, S. / Demetres, D. / Leonidas, G. / Swaminathan, J. / Maglione, D. / Battisti, M. / Tucci, M. / Persico, G. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rv6.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rv6.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rv6_validation.pdf.gz | 726.8 KB | Display | wwPDB validaton report |
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Full document | 1rv6_full_validation.pdf.gz | 733.2 KB | Display | |
Data in XML | 1rv6_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1rv6_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/1rv6 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rv6 | HTTPS FTP |
-Related structure data
Related structure data | 1fltS 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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Unit cell |
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-Components
#1: Protein | Mass: 11609.339 Da / Num. of mol.: 2 / Fragment: Receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P49763 #2: Protein | Mass: 11451.219 Da / Num. of mol.: 2 / Fragment: domain-2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P17948 #3: Chemical | ChemComp-B3P / | #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: 2.68 Å3/Da / Density % sol: 53.73 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→25 Å / Num. all: 17048 / Num. obs: 15482 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.046 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.45→2.54 Å / Rsym value: 0.161 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 72785 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.161 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FLT Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.654 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.514 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.659 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.5 Å / Total num. of bins used: 25 /
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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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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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