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- PDB-4wv1: Crystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3 -

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Basic information

Entry
Database: PDB / ID: 4wv1
TitleCrystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Fibroblast growth factor receptor 2
KeywordsTRANSFERASE/IMMUNE SYSTEM / FGFR2 / Fab / Complex / Antibody / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development ...Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / embryonic organ morphogenesis / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / embryonic pattern specification / outflow tract septum morphogenesis / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / digestive tract development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / bone morphogenesis / skeletal system morphogenesis / odontogenesis / ureteric bud development / positive regulation of mesenchymal cell proliferation / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / fibroblast growth factor binding / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / bone mineralization / prostate epithelial cord elongation / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / fibroblast growth factor receptor signaling pathway / embryonic organ development / cell fate commitment / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / cellular response to retinoic acid / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / post-embryonic development / regulation of ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / Negative regulation of FGFR2 signaling / animal organ morphogenesis / lung development / bone development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of canonical Wnt signaling pathway
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.362 Å
AuthorsYin, Y. / Carter, P.J.
CitationJournal: Mol.Cancer Ther. / Year: 2015
Title: Redesigning a Monospecific Anti-FGFR3 Antibody to Add Selectivity for FGFR2 and Expand Antitumor Activity.
Authors: Yin, Y. / Djakovic, S. / Marsters, S. / Tien, J. / Peng, J. / Tremayne, J. / Lee, G. / Neve, R.M. / Wu, Y. / Merchant, M. / Ashkenazi, A. / Carter, P.J.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Derived calculations
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Fibroblast growth factor receptor 2
C: Fibroblast growth factor receptor 2
B: Fab heavy chain
E: Fab heavy chain
A: Fab light chain
D: Fab light chain


Theoretical massNumber of molelcules
Total (without water)118,2946
Polymers118,2946
Non-polymers00
Water2,684149
1
F: Fibroblast growth factor receptor 2
E: Fab heavy chain
D: Fab light chain


Theoretical massNumber of molelcules
Total (without water)59,1473
Polymers59,1473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-27 kcal/mol
Surface area24040 Å2
MethodPISA
2
C: Fibroblast growth factor receptor 2
B: Fab heavy chain
A: Fab light chain


Theoretical massNumber of molelcules
Total (without water)59,1473
Polymers59,1473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-25 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.087, 181.239, 94.427
Angle α, β, γ (deg.)90.00, 113.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fibroblast growth factor receptor 2 / / FGFR-2 / K-sam / KGFR / Keratinocyte growth factor receptor


Mass: 11494.089 Da / Num. of mol.: 2 / Fragment: UNP residues 153-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 24344.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab light chain / Fragment antigen-binding


Mass: 23308.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 51.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→45.64 Å / Num. obs: 46583 / % possible obs: 98 % / Redundancy: 2.5 % / Rsym value: 0.094 / Net I/σ(I): 14.4
Reflection shellResolution: 2.36→2.47 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.9 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3GRW and 3CU1

3grw

3cu1


Resolution: 2.362→45.64 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 2367 5.08 %
Rwork0.1983 --
obs0.2007 46583 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.362→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8222 0 0 149 8371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098426
X-RAY DIFFRACTIONf_angle_d1.21211436
X-RAY DIFFRACTIONf_dihedral_angle_d14.1293020
X-RAY DIFFRACTIONf_chiral_restr0.0511274
X-RAY DIFFRACTIONf_plane_restr0.0061462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3624-2.41060.36371160.28372245X-RAY DIFFRACTION85
2.4106-2.4630.32361580.2742621X-RAY DIFFRACTION99
2.463-2.52030.31381430.25322649X-RAY DIFFRACTION99
2.5203-2.58330.30291460.23962618X-RAY DIFFRACTION99
2.5833-2.65310.28311390.23842659X-RAY DIFFRACTION99
2.6531-2.73120.30871460.21942638X-RAY DIFFRACTION99
2.7312-2.81930.28491360.2232644X-RAY DIFFRACTION99
2.8193-2.92010.26421220.22332665X-RAY DIFFRACTION99
2.9201-3.0370.30351520.22372619X-RAY DIFFRACTION99
3.037-3.17520.26951440.21892633X-RAY DIFFRACTION98
3.1752-3.34250.3021190.2172630X-RAY DIFFRACTION99
3.3425-3.55190.23521220.2042611X-RAY DIFFRACTION98
3.5519-3.8260.22511470.19392608X-RAY DIFFRACTION98
3.826-4.21080.22761380.17632594X-RAY DIFFRACTION97
4.2108-4.81950.20071310.15072599X-RAY DIFFRACTION97
4.8195-6.06980.18071410.16022591X-RAY DIFFRACTION97
6.0698-45.64850.20111670.17722592X-RAY DIFFRACTION96

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