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- PDB-3ojm: Crystal Structure of FGF1 complexed with the ectodomain of FGFR2b... -

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Basic information

Entry
Database: PDB / ID: 3ojm
TitleCrystal Structure of FGF1 complexed with the ectodomain of FGFR2b harboring P253R Apert 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 / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / 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 / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / embryonic organ morphogenesis / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / regulation of endothelial tube morphogenesis / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / FGFR3b ligand binding and activation / gland morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / branching involved in prostate gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / branching involved in salivary gland morphogenesis / outflow tract septum morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / positive regulation of hepatocyte proliferation / bone morphogenesis / S100 protein binding / skeletal system morphogenesis / odontogenesis / positive regulation of intracellular signal transduction / positive regulation of mesenchymal cell proliferation / ventricular cardiac muscle tissue morphogenesis / ureteric bud development / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / midbrain development / organ growth / inner ear morphogenesis / hair follicle morphogenesis / PI-3K cascade:FGFR3 / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / fibroblast growth factor binding / PI-3K cascade:FGFR2 / positive regulation of sprouting angiogenesis / bone mineralization / PI-3K cascade:FGFR4 / prostate epithelial cord elongation / PI-3K cascade:FGFR1 / positive regulation of cell division / excitatory synapse / PI3K Cascade / positive regulation of Wnt signaling pathway
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 / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...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 / 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. / 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 / 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 1 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 23, 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

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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: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7325
Polymers43,4442
Non-polymers2883
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-47 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.740, 72.349, 91.912
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 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.: 1
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: 25961.326 Da / Num. of mol.: 1 / Fragment: FGFR2b / Mutation: P253R
Source method: isolated from a genetically manipulated source
Details: This receptor harbors the P253R mutation responsible for Apert Syndrome. In the structure, the substituted arginine 253 sidechain makes additional hydrogen bonds with FGF1
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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 22% monomethyl ether PEG5000, 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: 0.92018 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2002
RadiationMonochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92018 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 27015 / Num. obs: 27015 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rsym value: 0.054 / Net I/σ(I): 40.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.1-2.1810.134.826220.103198.6
2.18-2.2610.439.526560.098198.9
2.26-2.3710.846.526340.087199
2.37-2.4911.455.326590.077199.5
2.49-2.6512.163.626820.072199.8
2.65-2.8512.778.826970.0641100
2.85-3.1413.595.127070.0571100
3.14-3.5913.9105.927390.0521100
3.59-4.5213.9109.227520.048199.6
4.52-3013.1105.428670.045199.1

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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: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 2605 RANDOM
Rwork0.229 --
all-26221 -
obs-26221 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.351 Å20 Å20 Å2
2--4.883 Å20 Å2
3----2.532 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 15 161 2950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_improper_angle_d0.796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.1-2.110.35440.24X-RAY DIFFRACTION455
2.11-2.130.4440.23X-RAY DIFFRACTION489
2.13-2.140.32540.24X-RAY DIFFRACTION456
2.14-2.160.25430.23X-RAY DIFFRACTION437
2.16-2.180.29550.24X-RAY DIFFRACTION463
2.18-2.190.29570.24X-RAY DIFFRACTION485
2.19-2.210.39560.24X-RAY DIFFRACTION432
2.21-2.230.36420.27X-RAY DIFFRACTION443
2.23-2.240.26660.24X-RAY DIFFRACTION452
2.24-2.260.25380.23X-RAY DIFFRACTION444

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