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- PDB-6j6y: FGFR4 D2 - Fab complex -

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Basic information

Entry
Database: PDB / ID: 6j6y
TitleFGFR4 D2 - Fab complex
Components
  • Fab Heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Fibroblast growth factor receptor 4
KeywordsTRANSFERASE/IMMUNE SYSTEM / Fab / TRANSFERASE-IMMUNE SYSTEM complex
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 / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / glucose homeostasis / PIP3 activates AKT signaling / 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 / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.15 Å
AuthorsTakahashi, M. / Hanzawa, H.
CitationJournal: Mol.Cancer Ther. / Year: 2019
Title: Preclinical Development of U3-1784, a Novel FGFR4 Antibody Against Cancer, and Avoidance of Its On-target Toxicity.
Authors: Bartz, R. / Fukuchi, K. / Ohtsuka, T. / Lange, T. / Gruner, K. / Watanabe, I. / Hayashi, S. / Oda, Y. / Kawaida, R. / Komori, H. / Kashimoto, Y. / Wirtz, P. / Mayer, J.A. / Redondo-Muller, M. ...Authors: Bartz, R. / Fukuchi, K. / Ohtsuka, T. / Lange, T. / Gruner, K. / Watanabe, I. / Hayashi, S. / Oda, Y. / Kawaida, R. / Komori, H. / Kashimoto, Y. / Wirtz, P. / Mayer, J.A. / Redondo-Muller, M. / Saito, S. / Takahashi, M. / Hanzawa, H. / Imai, E. / Martinez, A. / Hanai, M. / Haussinger, D. / Chapman, R.W. / Agatsuma, T. / Bange, J. / Abraham, R.
History
DepositionJan 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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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: Fab Heavy chain
C: Fab light chain
D: Fibroblast growth factor receptor 4
E: Fab Heavy chain
F: Fab light chain


Theoretical massNumber of molelcules
Total (without water)128,4676
Polymers128,4676
Non-polymers00
Water8,197455
1
A: Fibroblast growth factor receptor 4
B: Fab Heavy chain
C: Fab light chain


Theoretical massNumber of molelcules
Total (without water)64,2333
Polymers64,2333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fibroblast growth factor receptor 4
E: Fab Heavy chain
F: Fab light chain


Theoretical massNumber of molelcules
Total (without water)64,2333
Polymers64,2333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.218, 119.165, 105.099
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-341-

HOH

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Components

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


Mass: 11903.556 Da / Num. of mol.: 2 / Fragment: domain2
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: Antibody Fab Heavy chain / Fragment antigen-binding


Mass: 26600.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#3: Antibody Fab light chain / Fragment antigen-binding


Mass: 25729.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.9M ammonium sulfate, 0.1M sodium acetate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.41 Å / Num. obs: 74039 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.112 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.142 / Rrim(I) all: 0.209 / Χ2: 1.02 / Net I/σ(I): 6.6 / Num. measured all: 408438
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.432 / Mean I/σ(I) obs: 0.9 / Num. measured obs: 17342 / Num. possible: 43499 / Num. unique obs: 4586 / CC1/2: 0.321 / Rpim(I) all: 1.298 / Rrim(I) all: 1.939 / Χ2: 1.08 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.341 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 3449 5 %RANDOM
Rwork0.193 ---
obs0.1963 65516 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 164.1 Å2 / Biso mean: 69.266 Å2 / Biso min: 42.32 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å2-0 Å2-0.39 Å2
2---2 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7955 0 0 455 8410
Biso mean---70.71 -
Num. residues----1061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0158172
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.76711149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47351053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02921.27307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.444151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3121538
X-RAY DIFFRACTIONr_chiral_restr0.0920.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216126
LS refinement shellResolution: 2.15→2.205 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 253 -
Rwork0.357 4811 -
all-5064 -
obs--100 %

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