[English] 日本語
Yorodumi
- PDB-8yq1: Linear form of FGF10 from Homo sapiens -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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 / metanephros morphogenesis / otic vesicle formation / embryonic camera-type eye development / lung epithelium 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 / tissue regeneration / limb bud formation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / positive regulation of epithelial cell proliferation involved in wound healing / smooth muscle cell differentiation / positive regulation of keratinocyte migration / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / induction of positive chemotaxis / organ induction / Downstream signaling of activated FGFR1 / embryonic pattern specification / Phospholipase C-mediated cascade: FGFR1 / metanephros development / Developmental Lineage of Pancreatic Acinar Cells / regulation of smoothened signaling pathway / positive regulation of ATP-dependent activity / pancreas development / endothelial cell proliferation / positive regulation of Ras protein signal transduction / protein localization to cell surface / positive regulation of vascular endothelial growth factor receptor signaling pathway / determination of left/right symmetry / positive regulation of peptidyl-tyrosine phosphorylation / hair follicle morphogenesis / negative regulation of epithelial cell differentiation / branching morphogenesis of an epithelial tube / PI-3K cascade:FGFR2 / positive regulation of Notch signaling pathway / positive chemotaxis / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / chemoattractant activity / odontogenesis of dentin-containing tooth / establishment of mitotic spindle orientation / thyroid gland development / white fat cell differentiation / somatic stem cell population maintenance / keratinocyte proliferation / PI3K Cascade / positive regulation of epithelial cell migration / blood vessel remodeling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway / 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 / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FRS-mediated FGFR2 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: To Be Published
Title: N-terminal helix formation and dimer-monomer shift of FGF10 is essential for FGF2b binding
Authors: Park, H.J. / Park, Y.S. / Lee, C.E. / Kang, L.W.
History
DepositionMar 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more