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- PDB-7n1j: Crystal structure of FGFR4 domain 3 in complex with a de novo-des... -

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Basic information

Entry
Database: PDB / ID: 7n1j
TitleCrystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder
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 / 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 DNA biosynthetic process / positive regulation of catalytic activity ...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 DNA biosynthetic process / positive regulation of catalytic activity / 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 / cell surface receptor protein tyrosine kinase signaling pathway / 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
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 ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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: 2.99 Å
AuthorsPark, J.S. / Lee, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Design of protein-binding proteins from the target structure alone.
Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. ...Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. / Phal, A. / Yang, A. / Kozodoy, L. / DeWitt, M. / Picton, L. / Miller, L. / Strauch, E.M. / DeBouver, N.D. / Pires, A. / Bera, A.K. / Halabiya, S. / Hammerson, B. / Yang, W. / Bernard, S. / Stewart, L. / Wilson, I.A. / Ruohola-Baker, H. / Schlessinger, J. / Lee, S. / Savvides, S.N. / Garcia, K.C. / Baker, D.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
1
A: Fibroblast growth factor receptor 4
B: Binder


Theoretical massNumber of molelcules
Total (without water)21,8082
Polymers21,8082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-14 kcal/mol
Surface area10450 Å2
MethodPISA
2
C: Fibroblast growth factor receptor 4
D: Binder


Theoretical massNumber of molelcules
Total (without water)21,8082
Polymers21,8082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-17 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.531, 107.531, 69.047
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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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)

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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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M MES (pH 6.0), 20% PEG 3,350

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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: 2.99→50 Å / Num. obs: 9194 / % possible obs: 98.7 % / Redundancy: 4.7 % / CC1/2: 0.998 / Net I/σ(I): 19.1
Reflection shellResolution: 2.99→3.17 Å / Num. unique obs: 1452 / CC1/2: 0.952

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Processing

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

1cvs


Resolution: 2.99→46.56 Å / SU ML: 0.1962 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.0254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 460 5 %
Rwork0.2086 8731 -
obs0.2099 9191 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.93 Å2
Refinement stepCycle: LAST / Resolution: 2.99→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 0 0 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282606
X-RAY DIFFRACTIONf_angle_d0.48063556
X-RAY DIFFRACTIONf_chiral_restr0.0397428
X-RAY DIFFRACTIONf_plane_restr0.0034453
X-RAY DIFFRACTIONf_dihedral_angle_d3.4415374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.420.28961520.23682883X-RAY DIFFRACTION98.57
3.42-4.310.24211530.21122906X-RAY DIFFRACTION99
4.32-46.560.20891550.19692942X-RAY DIFFRACTION98.44

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