[English] 日本語
Yorodumi
- PDB-5w59: Crystal structure of a monomeric human FGF9 in complex with the e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w59
TitleCrystal structure of a monomeric human FGF9 in complex with the ectodomain of human FGFR1c
Components
  • Fibroblast growth factor 9
  • Fibroblast growth factor receptor 1
KeywordsCYTOKINE / Growth factor / Growth Factor Receptor / ligand-receptor complex
Function / homology
Function and homology information


regulation of timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / positive regulation of reproductive process / Sertoli cell proliferation / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions ...regulation of timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / positive regulation of reproductive process / Sertoli cell proliferation / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / diphosphate metabolic process / Transcriptional regulation of testis differentiation / ventricular zone neuroblast division / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / FGFR3b ligand binding and activation / embryonic skeletal system development / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / response to sodium phosphate / auditory receptor cell development / Epithelial-Mesenchymal Transition (EMT) during gastrulation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / chordate embryonic development / positive regulation of parathyroid hormone secretion / fibroblast growth factor receptor activity / eye development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / embryonic digestive tract development / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR3 / positive regulation of phospholipase activity / mesenchymal cell proliferation / paraxial mesoderm development / fibroblast growth factor receptor binding / lung-associated mesenchyme development / FGFR4 ligand binding and activation / male sex determination / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / activin receptor signaling pathway / Signaling by activated point mutants of FGFR1 / organ induction / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cell projection assembly / positive regulation of smoothened signaling pathway / cellular response to fibroblast growth factor stimulus / positive regulation of vascular associated smooth muscle cell migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / skeletal system morphogenesis / outer ear morphogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / embryonic limb morphogenesis / inner ear morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / midbrain development / cardiac muscle cell proliferation / smoothened signaling pathway / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / fibroblast growth factor binding / regulation of cell differentiation / PI-3K cascade:FGFR4 / negative regulation of Wnt signaling pathway / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / Formation of paraxial mesoderm / phosphatidylinositol-mediated signaling / positive regulation of cell division / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / canonical Wnt signaling pathway / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / cell maturation / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Immunoglobulin / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Immunoglobulin / 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. / 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 / 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 receptor 1 / Fibroblast growth factor 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsMohammadi, M. / Ma, J. / Liu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE13686 United States
CitationJournal: Structure / Year: 2017
Title: Regulation of Receptor Binding Specificity of FGF9 by an Autoinhibitory Homodimerization.
Authors: Liu, Y. / Ma, J. / Beenken, A. / Srinivasan, L. / Eliseenkova, A.V. / Mohammadi, M.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor 9
B: Fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7195
Polymers45,4312
Non-polymers2883
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-60 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.159, 86.793, 136.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fibroblast growth factor 9 / FGF-9 / Glia-activating factor / GAF / Heparin-binding growth factor 9 / HBGF-9


Mass: 19994.564 Da / Num. of mol.: 1 / Fragment: UNP residues 35-208 / Mutation: D195A/L204A/L205A
Source method: isolated from a genetically manipulated source
Details: Human FGF9 carrying D195A/L204A/L205A triple mutation in its C-terminal tail that renders the ligand monomeric
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF9 / Production host: Escherichia coli (E. coli) / References: UniProt: P31371
#2: Protein Fibroblast growth factor receptor 1 / FGFR-1 / Basic fibroblast growth factor receptor 1 / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 ...FGFR-1 / Basic fibroblast growth factor receptor 1 / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 / N-sam / Proto-oncogene c-Fgr


Mass: 25436.053 Da / Num. of mol.: 1
Fragment: Extracellular ligand binding domain of the "c" splice isoform (UNP residues 142-365)
Source method: isolated from a genetically manipulated source
Details: Ectodomain of human FGFR1c encompassing the membrane proximal D2 and D3 region
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR / Production host: Escherichia coli (E. coli)
References: UniProt: P11362, receptor protein-tyrosine kinase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, pH 8.0, 8% w/v PEG20000, 0.3 M sodium chloride, 40 mM L-proline

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18063 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.087 / Net I/σ(I): 29.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4 / Num. unique obs: 867 / Rsym value: 0.378 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OJV
Resolution: 2.498→29.527 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1799 9.99 %Random
Rwork0.1709 ---
obs0.176 18002 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.498→29.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 15 90 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082926
X-RAY DIFFRACTIONf_angle_d0.9563965
X-RAY DIFFRACTIONf_dihedral_angle_d6.9041737
X-RAY DIFFRACTIONf_chiral_restr0.056422
X-RAY DIFFRACTIONf_plane_restr0.006506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4981-2.56560.31181330.21351197X-RAY DIFFRACTION98
2.5656-2.64110.28241360.20761216X-RAY DIFFRACTION98
2.6411-2.72630.30461320.20711198X-RAY DIFFRACTION99
2.7263-2.82370.24421380.20381245X-RAY DIFFRACTION99
2.8237-2.93660.28731360.19941218X-RAY DIFFRACTION100
2.9366-3.07010.27171350.1931215X-RAY DIFFRACTION99
3.0701-3.23180.26731380.20191249X-RAY DIFFRACTION99
3.2318-3.4340.2691370.19851232X-RAY DIFFRACTION100
3.434-3.69870.22321390.17811244X-RAY DIFFRACTION100
3.6987-4.070.21031390.15291259X-RAY DIFFRACTION100
4.07-4.6570.15261420.13461278X-RAY DIFFRACTION100
4.657-5.85980.18581430.14171283X-RAY DIFFRACTION100
5.8598-29.52880.19361510.1651369X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1717-0.2697-0.41050.4969-0.3020.75890.0646-0.02160.18720.0255-0.12180.0962-0.0367-0.0212-00.2147-0.0075-0.0040.25790.03640.2935-8.58418.570248.8498
2-0.1641-0.1454-0.04741.1492-0.64920.67920.08-0.02350.034-0.0229-0.04650.02750.1030.09150.00440.1753-0.011-0.01040.25840.03660.21437.264910.011146.2327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 58 through 203)
2X-RAY DIFFRACTION2(chain 'B' and resid 147 through 360)

+
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