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- PDB-9u3n: Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F ... -

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Basic information

Entry
Database: PDB / ID: 9u3n
TitleCrystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-01
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / FGFR2
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 / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / 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 / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / bud elongation involved in lung branching / epidermis morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / reproductive structure development / limb bud formation / membranous septum morphogenesis / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in labyrinthine layer morphogenesis / mesenchymal cell proliferation involved in lung development / pyramidal neuron development / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / regulation of osteoblast proliferation / branching involved in salivary gland morphogenesis / embryonic pattern specification / positive regulation of phospholipase activity / lung-associated mesenchyme development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / mesodermal cell differentiation / bone morphogenesis / digestive tract development / skeletal system morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / inner ear morphogenesis / organ growth / hair follicle morphogenesis / Signaling by FGFR2 IIIa TM / ventricular cardiac muscle tissue morphogenesis / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of osteoblast differentiation / PI-3K cascade:FGFR2 / lung alveolus development / prostate epithelial cord elongation / midbrain development / bone mineralization / fibroblast growth factor binding / positive regulation of cell division / excitatory synapse / PI3K Cascade / positive regulation of Wnt signaling pathway / cell fate commitment / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / embryonic organ development / regulation of ERK1 and ERK2 cascade / SHC-mediated cascade:FGFR2 / positive regulation of cardiac muscle cell proliferation / cellular response to transforming growth factor beta stimulus / FRS-mediated FGFR2 signaling / cellular response to retinoic acid / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / positive regulation of epithelial cell proliferation / post-embryonic development / animal organ morphogenesis / Negative regulation of FGFR2 signaling / lung development / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity
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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsChen, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82422068 China
CitationJournal: To Be Published
Title: Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-1
Authors: Chen, L.
History
DepositionMar 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2354
Polymers71,3382
Non-polymers8972
Water00
1
A: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1182
Polymers35,6691
Non-polymers4481
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1182
Polymers35,6691
Non-polymers4481
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.069, 88.713, 127.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35669.121 Da / Num. of mol.: 2 / Mutation: V564F
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: Chemical ChemComp-A1ENT / ~{N}-[4-[4-azanyl-7-methyl-5-[2-(3-methylimidazo[4,5-b]pyridin-6-yl)ethynyl]pyrrolo[2,3-d]pyrimidin-6-yl]phenyl]prop-2-enamide


Mass: 448.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H20N8O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium formate, 20% PEG3,3500+16% Glutaric acid, 0.16% Mellitic acid, 0.16% Oxalic acid, 0.16% Pimelic acid, 0.16% Sebacic acid,0.16% trans-Cinnamic acid, 0.02 M HEPES Na pH6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.25→47.67 Å / Num. obs: 10510 / % possible obs: 89.9 % / Redundancy: 5 % / CC1/2: 0.981 / Net I/σ(I): 5.2
Reflection shellResolution: 3.25→3.51 Å / Num. unique obs: 2191 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→47.67 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.788 / SU B: 60.042 / SU ML: 0.896 / Cross valid method: FREE R-VALUE / ESU R Free: 0.787
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3419 560 5.343 %
Rwork0.2793 9921 -
all0.283 --
obs-10481 88.943 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 87.518 Å2
Baniso -1Baniso -2Baniso -3
1--6.436 Å20 Å2-0 Å2
2--4.794 Å2-0 Å2
3---1.641 Å2
Refinement stepCycle: LAST / Resolution: 3.25→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 68 0 4440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124542
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164354
X-RAY DIFFRACTIONr_angle_refined_deg0.8691.8496133
X-RAY DIFFRACTIONr_angle_other_deg0.3371.77710053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.84534
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.12552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80710826
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.241102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg7.81210199
X-RAY DIFFRACTIONr_chiral_restr0.0420.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
X-RAY DIFFRACTIONr_nbd_refined0.2130.21093
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24464
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22217
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.28
X-RAY DIFFRACTIONr_nbd_other0.220.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4030.22
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_mcbond_it1.7448.7682186
X-RAY DIFFRACTIONr_mcbond_other1.7448.7682186
X-RAY DIFFRACTIONr_mcangle_it3.12315.7652722
X-RAY DIFFRACTIONr_mcangle_other3.12315.7652723
X-RAY DIFFRACTIONr_scbond_it1.4578.8532356
X-RAY DIFFRACTIONr_scbond_other1.4568.8552357
X-RAY DIFFRACTIONr_scangle_it2.67716.2953411
X-RAY DIFFRACTIONr_scangle_other2.67716.2953412
X-RAY DIFFRACTIONr_lrange_it5.58481.5435227
X-RAY DIFFRACTIONr_lrange_other5.58381.5445228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.3340.379360.388745X-RAY DIFFRACTION92.2078
3.334-3.4250.452410.372708X-RAY DIFFRACTION89.8082
3.425-3.5240.445450.356700X-RAY DIFFRACTION91.9753
3.524-3.6320.346300.358672X-RAY DIFFRACTION90.5806
3.632-3.750.328300.31667X-RAY DIFFRACTION90.285
3.75-3.8810.329460.297611X-RAY DIFFRACTION89.5095
3.881-4.0260.388400.297589X-RAY DIFFRACTION89.6011
4.026-4.190.387350.262596X-RAY DIFFRACTION88.9986
4.19-4.3740.391330.258536X-RAY DIFFRACTION88.4914
4.374-4.5860.275270.249533X-RAY DIFFRACTION88.3281
4.586-4.8310.248340.238501X-RAY DIFFRACTION88.7231
4.831-5.1210.314230.264492X-RAY DIFFRACTION88.7931
5.121-5.470.421260.285453X-RAY DIFFRACTION87.5686
5.47-5.9020.26230.291422X-RAY DIFFRACTION87.4263
5.902-6.4560.386270.246399X-RAY DIFFRACTION88.3817
6.456-7.2010.318160.231351X-RAY DIFFRACTION86.3529
7.201-8.2840.218160.234312X-RAY DIFFRACTION85.8639
8.284-10.070.279130.219275X-RAY DIFFRACTION85.4599
10.07-13.9340.36130.218220X-RAY DIFFRACTION85.0365
13.934-47.670.34860.358139X-RAY DIFFRACTION81.0056

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