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- PDB-7tyd: Crystal structure of FGFR4 domain 3 in complex with a de novo-des... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tyd | ||||||
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Title | Crystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder in P21 space group | ||||||
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![]() | SIGNALING PROTEIN / Receptor tyrosine kinase / Complex / Binder / MEMBRANE PROTEIN | ||||||
Function / homology | ![]() FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / positive regulation of catalytic activity / positive regulation of DNA biosynthetic process ...FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / positive regulation of catalytic activity / positive regulation of DNA biosynthetic process / fibroblast growth factor binding / PI-3K cascade:FGFR4 / positive regulation of proteolysis / regulation of lipid metabolic process / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / transport vesicle / FRS-mediated FGFR4 signaling / cholesterol homeostasis / Negative regulation of FGFR4 signaling / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / glucose homeostasis / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / receptor complex / endosome / positive regulation of cell population proliferation / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, J.S. / Lee, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Isoform-specific inhibition of FGFR signaling achieved by a de-novo-designed mini-protein. Authors: Park, J.S. / Choi, J. / Cao, L. / Mohanty, J. / Suzuki, Y. / Park, A. / Baker, D. / Schlessinger, J. / Lee, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cvsS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 14271.884 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22455, receptor protein-tyrosine kinase #2: Protein | Mass: 7535.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris (pH 5.5) 25% polyethylene glycol 3,350 3% 1,5-diaminopentane dihydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 8780 / % possible obs: 96.1 % / Redundancy: 4.9 % / CC1/2: 0.992 / Net I/σ(I): 18.55 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.564 / Num. unique obs: 412 / CC1/2: 0.889 / % possible all: 87.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CVS Resolution: 2.86→49.32 Å / SU ML: 0.4751 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 37.347 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.09 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.86→49.32 Å
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Refine LS restraints |
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LS refinement shell |
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