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- PDB-1nun: Crystal Structure Analysis of the FGF10-FGFR2b Complex -

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Basic information

Entry
Database: PDB / ID: 1nun
TitleCrystal Structure Analysis of the FGF10-FGFR2b Complex
Components
  • Fibroblast growth factor-10
  • fibroblast growth factor receptor 2 isoform 2
KeywordsHORMONE/GROWTH FACTOR/MEMBRANE PROTEIN / BETA-TREFOIL FOLD / IMMUNOGLOBULIN-LIKE DOMAIN / HORMONE-GROWTH FACTOR-MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


bronchiole morphogenesis / mesenchymal-epithelial cell signaling involved in lung development / lung proximal/distal axis specification / tear secretion / positive regulation of white fat cell proliferation / positive regulation of hair follicle cell proliferation / embryonic genitalia morphogenesis / urothelial cell proliferation / positive regulation of urothelial cell proliferation / secretion by lung epithelial cell involved in lung growth ...bronchiole morphogenesis / mesenchymal-epithelial cell signaling involved in lung development / lung proximal/distal axis specification / tear secretion / positive regulation of white fat cell proliferation / positive regulation of hair follicle cell proliferation / embryonic genitalia morphogenesis / urothelial cell proliferation / positive regulation of urothelial cell proliferation / secretion by lung epithelial cell involved in lung growth / regulation of activin receptor signaling pathway / type 2 fibroblast growth factor receptor binding / semicircular canal fusion / white fat cell proliferation / muscle cell fate commitment / salivary gland development / fibroblast growth factor receptor apoptotic signaling pathway / type II pneumocyte differentiation / Harderian gland development / lung saccule development / prostatic bud formation / radial glial cell differentiation / Regulation of gene expression in early pancreatic precursor cells / regulation of saliva secretion / FGFRL1 modulation of FGFR1 signaling / female genitalia morphogenesis / submandibular salivary gland formation / 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 / bud outgrowth involved in lung branching / lacrimal gland development / prostate gland morphogenesis / metanephros morphogenesis / otic vesicle formation / embryonic camera-type eye development / regulation of smooth muscle cell differentiation / lung epithelium development / positive regulation of keratinocyte proliferation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / positive regulation of lymphocyte proliferation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / pituitary gland development / endochondral bone growth / morphogenesis of embryonic epithelium / male genitalia morphogenesis / bud elongation involved in lung branching / epidermis morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / mesonephros development / tissue regeneration / reproductive structure development / limb bud formation / membranous septum morphogenesis / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / 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 / positive regulation of epithelial cell proliferation involved in wound healing / smooth muscle cell differentiation / branching involved in labyrinthine layer morphogenesis / mesenchymal cell proliferation involved in lung development / pyramidal neuron development / positive regulation of keratinocyte migration / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / regulation of osteoblast proliferation / FGFR1b ligand binding and activation / induction of positive chemotaxis / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / embryonic pattern specification / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / outflow tract septum morphogenesis / metanephros development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / mesodermal cell differentiation / positive regulation of ATP-dependent activity
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin domain ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 10 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsYeh, B.K. / Igarashi, M. / Eliseenkova, A.V. / Plotnikov, A.N. / Sher, I. / Ron, D. / Aaronson, S.A. / Mohammadi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural basis by which alternative splicing confers specificity in fibroblast growth factor receptors.
Authors: Yeh, B.K. / Igarashi, M. / Eliseenkova, A.V. / Plotnikov, A.N. / Sher, I. / Ron, D. / Aaronson, S.A. / Mohammadi, M.
History
DepositionJan 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor-10
B: fibroblast growth factor receptor 2 isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4935
Polymers42,7712
Non-polymers1,7223
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-33 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.930, 113.930, 164.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Fibroblast growth factor-10 / FGF-10 / keratinocyte growth factor receptor / K-sam protein / protein tyrosine kinase / receptor ...FGF-10 / keratinocyte growth factor receptor / K-sam protein / protein tyrosine kinase / receptor like 14 / FGF receptor / bacteria-expressed kinase / fibroblast growth factor receptor BEK / tyrosylprotein kinase / hydroxyaryl-protein kinase


Mass: 16813.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF10 / Plasmid: pET-9c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O15520
#2: Protein fibroblast growth factor receptor 2 isoform 2


Mass: 25957.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21802
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 %PEG4001reservoir
22.0 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH8.5
47 mg/mlprotein1drop
525 mMHEPES1droppH7.5
6150 mM1dropNaCl

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97880, 0.97933, 0.97169
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2001
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.979331
30.971691
ReflectionResolution: 2.9→25 Å / Num. all: 26231 / Num. obs: 15965 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3.14 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 14520 / Num. measured all: 279164 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.279

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→25 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1477 9.3 %RANDOM
Rwork0.239 ---
all0.234 26231 --
obs0.232 14520 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0623 Å2 / ksol: 0.290463 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å25.18 Å20 Å2
2---0.69 Å20 Å2
3---1.37 Å2
Refine analyzeLuzzati coordinate error free: 0.47 Å / Luzzati sigma a free: 0.64 Å
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 29 25 2727
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.893
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it7.672
X-RAY DIFFRACTIONc_scangle_it9.042.5
LS refinement shellHighest resolution: 2.9 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork2422 -
Rfree-8.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION415P_PAR.TXT15P_TOP.TXT
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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