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- PDB-7tyd: Crystal structure of FGFR4 domain 3 in complex with a de novo-des... -

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Basic information

Entry
Database: PDB / ID: 7tyd
TitleCrystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder in P21 space group
Components
  • Binder
  • Fibroblast growth factor receptor 4
KeywordsSIGNALING PROTEIN / Receptor tyrosine kinase / Complex / Binder / MEMBRANE PROTEIN
Function / homology
Function and homology information


FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / positive regulation of catalytic activity / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / fibroblast growth factor receptor activity / positive regulation of DNA biosynthetic process ...FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / positive regulation of catalytic activity / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / fibroblast growth factor receptor activity / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR4 / fibroblast growth factor binding / regulation of lipid metabolic process / positive regulation of proteolysis / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / transport vesicle / FRS-mediated FGFR4 signaling / peptidyl-tyrosine phosphorylation / cholesterol homeostasis / Negative regulation of FGFR4 signaling / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / glucose homeostasis / PIP3 activates AKT signaling / heparin binding / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of ERK1 and ERK2 cascade / receptor complex / endosome / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum / Golgi apparatus / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Fibroblast growth factor receptor family / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. ...Fibroblast growth factor receptor family / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Fibroblast growth factor receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsPark, J.S. / Lee, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
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
DepositionFeb 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 4
B: Binder
C: Fibroblast growth factor receptor 4
D: Binder


Theoretical massNumber of molelcules
Total (without water)43,6154
Polymers43,6154
Non-polymers00
Water1086
1
A: Fibroblast growth factor receptor 4
B: Binder


Theoretical massNumber of molelcules
Total (without water)21,8082
Polymers21,8082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-16 kcal/mol
Surface area8280 Å2
MethodPISA
2
C: Fibroblast growth factor receptor 4
D: Binder


Theoretical massNumber of molelcules
Total (without water)21,8082
Polymers21,8082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-16 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.798, 58.664, 68.055
Angle α, β, γ (deg.)90.000, 110.926, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fibroblast growth factor receptor 4 / FGFR-4


Mass: 14271.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR4, JTK2, TKF / Production host: Escherichia coli (E. coli)
References: UniProt: P22455, receptor protein-tyrosine kinase
#2: Protein Binder


Mass: 7535.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CVS

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
RfactorNum. reflection% reflection
Rfree0.3063 443 5.07 %
Rwork0.2684 8290 -
obs0.2704 8733 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.09 Å2
Refinement stepCycle: LAST / Resolution: 2.86→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 0 6 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272205
X-RAY DIFFRACTIONf_angle_d0.54573029
X-RAY DIFFRACTIONf_chiral_restr0.0391382
X-RAY DIFFRACTIONf_plane_restr0.003379
X-RAY DIFFRACTIONf_dihedral_angle_d4.2565325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.270.37891440.30942731X-RAY DIFFRACTION95.14
3.27-4.120.31641500.27882814X-RAY DIFFRACTION97.44
4.12-49.320.27721490.24882745X-RAY DIFFRACTION94.05

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