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- PDB-8yq1: Linear form of FGF10 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 8yq1
TitleLinear form of FGF10 from Homo sapiens
ComponentsFibroblast growth factor 10
KeywordsHORMONE / Growth Factor / FGF10 / Fibroblast
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 / submandibular salivary gland formation ...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 / submandibular salivary gland formation / 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 / lung saccule development / fibroblast growth factor receptor apoptotic signaling pathway / Harderian gland 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 / 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 / type II pneumocyte differentiation / metanephros morphogenesis / otic vesicle formation / lung epithelium development / embryonic camera-type eye development / positive regulation of keratinocyte proliferation / positive regulation of lymphocyte proliferation / pituitary gland development / male genitalia morphogenesis / bud elongation involved in lung branching / mesonephros development / limb bud formation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / embryonic digestive tract morphogenesis / positive regulation of epithelial cell proliferation involved in wound healing / epithelial cell proliferation involved in salivary gland morphogenesis / smooth muscle cell differentiation / FGFR2b ligand binding and activation / positive regulation of keratinocyte migration / fibroblast growth factor receptor binding / Activated point mutants of FGFR2 / tissue regeneration / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / induction of positive chemotaxis / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / embryonic pattern specification / positive regulation of ATP-dependent activity / metanephros development / Developmental Lineage of Pancreatic Acinar Cells / regulation of smoothened signaling pathway / pancreas development / positive regulation of Ras protein signal transduction / endothelial cell proliferation / determination of left/right symmetry / positive regulation of vascular endothelial growth factor receptor signaling pathway / protein localization to cell surface / positive regulation of peptidyl-tyrosine phosphorylation / hair follicle morphogenesis / negative regulation of epithelial cell differentiation / PI-3K cascade:FGFR2 / branching morphogenesis of an epithelial tube / positive chemotaxis / positive regulation of Notch signaling pathway / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / chemoattractant activity / odontogenesis of dentin-containing tooth / thyroid gland development / establishment of mitotic spindle orientation / white fat cell differentiation / PI3K Cascade / positive regulation of epithelial cell migration / keratinocyte proliferation / somatic stem cell population maintenance / blood vessel remodeling / fibroblast growth factor receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / vascular endothelial growth factor receptor signaling pathway / SHC-mediated cascade:FGFR2 / negative regulation of stem cell proliferation / SHC-mediated cascade:FGFR1 / spleen development / FRS-mediated FGFR2 signaling / FRS-mediated FGFR1 signaling
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF
Similarity search - Domain/homology
Fibroblast growth factor 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsPark, H.J. / Park, Y.S. / Lee, C.E. / Kang, L.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentKS171094 Korea, Republic Of
CitationJournal: Febs J. / Year: 2025
Title: N-terminal helix formation and dimer-monomer transition of FGF10 in specific recognition of FGFR2b.
Authors: Park, H. / Park, Y.S. / Kwak, K. / Yun, J. / Lee, H. / Lee, C.E. / Lee, D. / Lee, K.W. / An, Y.J. / Yim, H.S. / Lee, J.H. / Cha, S.S. / Kang, L.W.
History
DepositionMar 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 10
B: Fibroblast growth factor 10


Theoretical massNumber of molelcules
Total (without water)33,0242
Polymers33,0242
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-9 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.845, 73.845, 227.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-336-

HOH

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Components

#1: Protein Fibroblast growth factor 10 / FGF-10 / Keratinocyte growth factor 2


Mass: 16511.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF10 / Plasmid: pET-29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta pLysS / References: UniProt: O15520
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Sulfate, 10% PEG 4000, 0.1 M Tris-HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Steady flow of liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.56→48.92 Å / Num. obs: 12263 / % possible obs: 97.46 % / Redundancy: 13.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.017 / Rrim(I) all: 0.071 / Rsym value: 0.069 / Net I/σ(I): 18.6
Reflection shellResolution: 2.56→2.65 Å / Rmerge(I) obs: 0.449 / Num. unique obs: 1143

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→48.92 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.863 / SU B: 10.772 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27771 605 4.9 %RANDOM
Rwork0.20154 ---
obs0.2053 11658 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.229 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.56→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 0 75 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0112257
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162072
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.673047
X-RAY DIFFRACTIONr_angle_other_deg0.5391.5874726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6645279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.439513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8710371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6573.9081122
X-RAY DIFFRACTIONr_mcbond_other3.6573.9091122
X-RAY DIFFRACTIONr_mcangle_it5.6497.0051399
X-RAY DIFFRACTIONr_mcangle_other5.6537.0081400
X-RAY DIFFRACTIONr_scbond_it4.5544.4881135
X-RAY DIFFRACTIONr_scbond_other4.5524.4931136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1467.9931649
X-RAY DIFFRACTIONr_long_range_B_refined10.13546.122501
X-RAY DIFFRACTIONr_long_range_B_other10.1245.882495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.563→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 43 -
Rwork0.255 800 -
obs--94.19 %

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