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- PDB-2p39: Crystal structure of human FGF23 -

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Basic information

Entry
Database: PDB / ID: 2p39
TitleCrystal structure of human FGF23
ComponentsFibroblast growth factor 23
KeywordsSIGNALING PROTEIN / atypical beta-trefoil fold
Function / homology
Function and homology information


type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of vitamin D 24-hydroxylase activity / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / negative regulation of hormone secretion / vitamin D catabolic process / response to sodium phosphate / intracellular phosphate ion homeostasis ...type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of vitamin D 24-hydroxylase activity / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / negative regulation of hormone secretion / vitamin D catabolic process / response to sodium phosphate / intracellular phosphate ion homeostasis / negative regulation of bone mineralization / phosphate ion homeostasis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / cellular response to vitamin D / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cellular response to leptin stimulus / cellular response to interleukin-6 / cellular response to parathyroid hormone stimulus / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / response to magnesium ion / PI3K Cascade / negative regulation of osteoblast differentiation / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / regulation of cell migration / ERK1 and ERK2 cascade / animal organ morphogenesis / Negative regulation of FGFR3 signaling / Post-translational protein phosphorylation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / growth factor activity / Golgi lumen / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
sucrose octasulfate / Fibroblast growth factor 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMohammadi, M.
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: Molecular insights into the klotho-dependent, endocrine mode of action of fibroblast growth factor 19 subfamily members.
Authors: Goetz, R. / Beenken, A. / Ibrahimi, O.A. / Kalinina, J. / Olsen, S.K. / Eliseenkova, A.V. / Xu, C. / Neubert, T.A. / Zhang, F. / Linhardt, R.J. / Yu, X. / White, K.E. / Inagaki, T. / ...Authors: Goetz, R. / Beenken, A. / Ibrahimi, O.A. / Kalinina, J. / Olsen, S.K. / Eliseenkova, A.V. / Xu, C. / Neubert, T.A. / Zhang, F. / Linhardt, R.J. / Yu, X. / White, K.E. / Inagaki, T. / Kliewer, S.A. / Yamamoto, M. / Kurosu, H. / Ogawa, Y. / Kuro-O, M. / Lanske, B. / Razzaque, M.S. / Mohammadi, M.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8392
Polymers17,8561
Non-polymers9831
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.811, 47.094, 84.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fibroblast growth factor 23 / FGF-23 / Tumor-derived hypophosphatemia-inducing factor


Mass: 17856.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF23, HYPF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLys-S / References: UniProt: Q9GZV9
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, 1.0 M (NH4)2SO4, 10 mM [Co(NH3)6]Cl3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2005
RadiationMonochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 25550 / Num. obs: 25550 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rsym value: 0.059 / Net I/σ(I): 26.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.7 % / Num. unique all: 2408 / Rsym value: 0.297 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P23

2p23


Resolution: 1.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2496 -Random
Rwork0.203 ---
all-25152 --
obs-25152 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.243 Å20 Å20 Å2
2--2.016 Å20 Å2
3---0.227 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 55 93 1261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005595
X-RAY DIFFRACTIONc_angle_d1.37432
X-RAY DIFFRACTIONc_improper_angle_d0.72625

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