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- PDB-3oj2: Crystal structure of FGF1 complexed with the ectodomain of FGFR2b... -

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Basic information

Entry
Database: PDB / ID: 3oj2
TitleCrystal structure of FGF1 complexed with the ectodomain of FGFR2b harboring the A172F Pfeiffer syndrome mutation
Components
  • Fibroblast growth factor receptor 2
  • Heparin-binding growth factor 1
KeywordsCytokine/Signaling Protein / beta trefoil motif / Immunoglobulin-like domain / growth factor / growth factor receptor / extracellular / Cytokine-Signaling Protein complex
Function / homology
Function and homology information


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 / lateral sprouting from an epithelium / 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 ...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 / lateral sprouting from an epithelium / 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 / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / mesonephric epithelium development / branch elongation involved in ureteric bud branching / bud elongation involved in lung branching / epidermis morphogenesis / regulation of endothelial tube morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / reproductive structure development / FGFR3b ligand binding and activation / limb bud formation / regulation of endothelial cell chemotaxis to fibroblast growth factor / membranous septum morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / positive regulation of phospholipase activity / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / epithelial cell proliferation involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation involved in lung development / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / branching involved in labyrinthine layer morphogenesis / lung lobe morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / regulation of osteoblast proliferation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / fibroblast growth factor receptor activity / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / embryonic pattern specification / pyramidal neuron development / embryonic cranial skeleton morphogenesis / lung-associated mesenchyme development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / mesodermal cell differentiation / bone morphogenesis / S100 protein binding / digestive tract development / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / skeletal system morphogenesis / organ growth / inner ear morphogenesis / hair follicle morphogenesis / Signaling by FGFR2 IIIa TM / lung alveolus development / PI-3K cascade:FGFR3 / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / prostate epithelial cord elongation / PI-3K cascade:FGFR1 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / positive regulation of sprouting angiogenesis / midbrain development / bone mineralization / fibroblast growth factor binding / positive regulation of MAP kinase activity / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / epithelial to mesenchymal transition / excitatory synapse / anatomical structure morphogenesis
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBeenken, A. / Mohammadi, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Plasticity in Interactions of Fibroblast Growth Factor 1 (FGF1) N Terminus with FGF Receptors Underlies Promiscuity of FGF1.
Authors: Beenken, A. / Eliseenkova, A.V. / Ibrahimi, O.A. / Olsen, S.K. / Mohammadi, M.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparin-binding growth factor 1
B: Heparin-binding growth factor 1
C: Fibroblast growth factor receptor 2
D: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4009
Polymers86,9204
Non-polymers4805
Water2,270126
1
A: Heparin-binding growth factor 1
C: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7485
Polymers43,4602
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-48 kcal/mol
Surface area16790 Å2
MethodPISA
2
B: Heparin-binding growth factor 1
D: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6524
Polymers43,4602
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-41 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.945, 77.945, 137.555
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 17482.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P05230
#2: Protein Fibroblast growth factor receptor 2 / FGFR-2 / Keratinocyte growth factor receptor / K-sam


Mass: 25977.344 Da / Num. of mol.: 2 / Mutation: A172F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BEK, FGFR2, KGFR, KSAM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P21802, receptor protein-tyrosine kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE MATCHES ISOFORM 3 OF UNIPROT ENTRY P21802 (RESIDUES 140 - 369, IDENTIFIER: P21802-3).

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 20% PEG4000, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.277 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2002
RadiationMonochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.277 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 47189 / Num. obs: 47189 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.048 / Net I/σ(I): 25.4
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.2-2.283.45.947320.265199.6
2.28-2.373.58.147600.1861100
2.37-2.483.511.647250.1361100
2.48-2.613.515.247980.1091100
2.61-2.773.522.247530.0811100
2.77-2.993.531.647320.0631100
2.99-3.293.541.347370.0511100
3.29-3.763.549.847490.0461100
3.76-4.733.453.347080.04199.3
4.73-303.350.944950.036194.1

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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 1NUN

1nun


Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 2287 RANDOM
Rwork0.262 --
all-45665 -
obs-45665 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.633 Å2-5.551 Å20 Å2
2---3.633 Å20 Å2
3---7.265 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 25 126 5523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.220.46410.36X-RAY DIFFRACTION958
2.22-2.230.4420.38X-RAY DIFFRACTION856
2.23-2.250.34490.35X-RAY DIFFRACTION952
2.25-2.270.42390.36X-RAY DIFFRACTION858
2.27-2.290.4500.36X-RAY DIFFRACTION979
2.29-2.310.37420.35X-RAY DIFFRACTION870
2.31-2.330.44440.35X-RAY DIFFRACTION950
2.33-2.350.33420.35X-RAY DIFFRACTION967
2.35-2.370.38530.35X-RAY DIFFRACTION952

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