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- PDB-1ii4: CRYSTAL STRUCTURE OF SER252TRP APERT MUTANT FGF RECEPTOR 2 (FGFR2... -

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Basic information

Entry
Database: PDB / ID: 1ii4
TitleCRYSTAL STRUCTURE OF SER252TRP APERT MUTANT FGF RECEPTOR 2 (FGFR2) IN COMPLEX WITH FGF2
Components
  • FIBROBLAST GROWTH FACTOR RECEPTOR 2
  • HEPARIN-BINDING GROWTH FACTOR 2
KeywordsGROWTH FACTOR/GROWTH FACTOR RECEPTOR / IMMUNOGLOBULIN LIKE DOMAIN / B-TREFOIL / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / 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 / chondroblast differentiation / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / lymphatic endothelial cell migration / chemokine binding / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / negative regulation of fibroblast growth factor receptor signaling pathway / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / embryonic organ morphogenesis / positive regulation of cerebellar granule cell precursor proliferation / endochondral bone growth / morphogenesis of embryonic epithelium / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / epidermis morphogenesis / bud elongation involved in lung branching / cerebellar granule cell precursor proliferation / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / positive regulation of stem cell differentiation / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / hyaluronan catabolic process / receptor-receptor interaction / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / regulation of endothelial cell chemotaxis to fibroblast growth factor / glial cell differentiation / embryonic digestive tract morphogenesis / inner ear auditory receptor cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of wound healing / mesenchymal cell differentiation / stem cell development / branching involved in prostate gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / mesenchymal cell proliferation involved in lung development / Phospholipase C-mediated cascade; FGFR3 / branching involved in labyrinthine layer morphogenesis / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of epithelial tube formation / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / Signaling by activated point mutants of FGFR1 / outflow tract septum morphogenesis / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / paracrine signaling / digestive tract development / mesodermal cell differentiation / negative regulation of fibroblast migration / regulation of smoothened signaling pathway / positive regulation of endothelial cell chemotaxis / embryonic cranial skeleton morphogenesis
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 2 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsIbrahimi, O.A. / Eliseenkova, A.V. / Plotnikov, A.N. / Ornitz, D.M. / Mohammadi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural basis for fibroblast growth factor receptor 2 activation in Apert syndrome.
Authors: Ibrahimi, O.A. / Eliseenkova, A.V. / Plotnikov, A.N. / Yu, K. / Ornitz, D.M. / Mohammadi, M.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: HEPARIN-BINDING GROWTH FACTOR 2
B: HEPARIN-BINDING GROWTH FACTOR 2
C: HEPARIN-BINDING GROWTH FACTOR 2
D: HEPARIN-BINDING GROWTH FACTOR 2
E: FIBROBLAST GROWTH FACTOR RECEPTOR 2
F: FIBROBLAST GROWTH FACTOR RECEPTOR 2
G: FIBROBLAST GROWTH FACTOR RECEPTOR 2
H: FIBROBLAST GROWTH FACTOR RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)167,9598
Polymers167,9598
Non-polymers00
Water0
1
A: HEPARIN-BINDING GROWTH FACTOR 2
E: FIBROBLAST GROWTH FACTOR RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)41,9902
Polymers41,9902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area15390 Å2
MethodPISA
2
B: HEPARIN-BINDING GROWTH FACTOR 2
F: FIBROBLAST GROWTH FACTOR RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)41,9902
Polymers41,9902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-16 kcal/mol
Surface area15380 Å2
MethodPISA
3
C: HEPARIN-BINDING GROWTH FACTOR 2
G: FIBROBLAST GROWTH FACTOR RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)41,9902
Polymers41,9902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area15390 Å2
MethodPISA
4
D: HEPARIN-BINDING GROWTH FACTOR 2
H: FIBROBLAST GROWTH FACTOR RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)41,9902
Polymers41,9902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.970, 72.657, 89.739
Angle α, β, γ (deg.)89.98, 89.70, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HEPARIN-BINDING GROWTH FACTOR 2 / FGF2 / HBGF-2 / BASIC FIBROBLAST GROWTH FACTOR / BFGF


Mass: 17249.732 Da / Num. of mol.: 4 / Mutation: C78S,C96S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P09038
#2: Protein
FIBROBLAST GROWTH FACTOR RECEPTOR 2 / / FGFR2 / KERATINOCYTE GROWTH FACTOR RECEPTOR


Mass: 24740.064 Da / Num. of mol.: 4
Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN CONSISTING OF IG-LIKE DOMAINS II (D2) AND III (D3), RESIDUES 147-366
Mutation: S252W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P21802, EC: 2.7.1.112

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Isopropanol, HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMHEPES-NaOH1drop
3150 mM1dropNaCl
410-15 %PEG40001reservoir
510 %isopropanol alcohol1reservoir
60.1 MHEPES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 74426 / Num. obs: 74426 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.25 / % possible all: 79.7
Reflection
*PLUS
Num. obs: 46770 / Num. measured all: 74426 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 79.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EV2

1ev2


Resolution: 2.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2307 4.7 %RANDOM
Rwork0.238 ---
obs0.238 46161 93.8 %-
all-46161 --
Solvent computationSolvent model: CNS / Bsol: 27.5 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.533 Å20 Å22.644 Å2
2---18.701 Å20 Å2
3---15.167 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10280 0 0 0 10280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.795
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.292
X-RAY DIFFRACTIONc_scangle_it2.042.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 4.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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