[English] 日本語
Yorodumi
- PDB-1nun: Crystal Structure Analysis of the FGF10-FGFR2b Complex -

+
Open data


ID or keywords:

Loading...

-
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


tear secretion / positive regulation of hair follicle cell proliferation / urothelial cell proliferation / positive regulation of urothelial cell proliferation / secretion by lung epithelial cell involved in lung growth / type 2 fibroblast growth factor receptor binding / salivary gland development / lung saccule development / bud outgrowth involved in lung branching / radial glial cell differentiation ...tear secretion / positive regulation of hair follicle cell proliferation / urothelial cell proliferation / positive regulation of urothelial cell proliferation / secretion by lung epithelial cell involved in lung growth / type 2 fibroblast growth factor receptor binding / salivary gland development / lung saccule development / bud outgrowth involved in lung branching / radial glial cell differentiation / Regulation of gene expression in early pancreatic precursor cells / FGFRL1 modulation of FGFR1 signaling / lung epithelium development / positive regulation of keratinocyte proliferation / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / prostate gland morphogenesis / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / lacrimal gland development / otic vesicle formation / bud elongation involved in lung branching / regulation of saliva secretion / regulation of smooth muscle cell differentiation / prostate epithelial cord elongation / lung lobe morphogenesis / regulation of morphogenesis of a branching structure / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in labyrinthine layer morphogenesis / orbitofrontal cortex development / morphogenesis of embryonic epithelium / positive regulation of lymphocyte proliferation / branching involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / epidermis morphogenesis / branching morphogenesis of a nerve / gland morphogenesis / embryonic organ morphogenesis / limb bud formation / endochondral bone growth / membranous septum morphogenesis / mesonephros development / reproductive structure development / embryonic digestive tract morphogenesis / positive regulation of epithelial cell proliferation involved in wound healing / positive regulation of epithelial cell proliferation involved in lung morphogenesis / tissue regeneration / organ growth / branching involved in prostate gland morphogenesis / metanephros development / epithelial cell proliferation / mesenchymal cell differentiation / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / fibroblast growth factor receptor binding / FGFR2b ligand binding and activation / positive regulation of phospholipase activity / positive regulation of mesenchymal cell proliferation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of keratinocyte migration / positive regulation of peptidyl-tyrosine phosphorylation / lung alveolus development / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / embryonic cranial skeleton morphogenesis / regulation of osteoblast proliferation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / fibroblast growth factor receptor activity / Developmental Lineage of Mammary Stem Cells / embryonic pattern specification / pyramidal neuron development / ureteric bud development / positive regulation of ATP-dependent activity / negative regulation of keratinocyte proliferation / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / hair follicle morphogenesis / skeletal system morphogenesis / post-embryonic development / inner ear morphogenesis / digestive tract development / mesodermal cell differentiation / protein localization to cell surface / bone morphogenesis / odontogenesis / branching morphogenesis of an epithelial tube / bone mineralization / embryonic organ development / midbrain development
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. / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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-IDDetails (eV)Chemical formula
13 %PEG4001reservoir
22.0 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH8.5
47 mg/mlprotein1drop
525 mMHEPES1droppH7.5
6150 mM1dropNaCl

-
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

-
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

+
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