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- PDB-2fdb: Crystal Structure of Fibroblast growth factor (FGF)8b in complex ... -

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Basic information

Entry
Database: PDB / ID: 2fdb
TitleCrystal Structure of Fibroblast growth factor (FGF)8b in complex with FGF Receptor (FGFR) 2c
Components
  • Fibroblast growth factor receptor 2
  • fibroblast growth factor 8 isoform B
KeywordsHORMONE/GROWTH FACTOR/TRANSFERASE / beta-trefoil fold / immunoglobulin fold / HORMONE-GROWTH FACTOR-TRANSFERASE COMPLEX
Function / homology
Function and homology information


pallium development / midbrain-hindbrain boundary development / negative regulation of cardiac muscle tissue development / subpallium development / larynx morphogenesis / neural plate morphogenesis / mesodermal cell migration / type 2 fibroblast growth factor receptor binding / cell migration involved in mesendoderm migration / mitotic nuclear division ...pallium development / midbrain-hindbrain boundary development / negative regulation of cardiac muscle tissue development / subpallium development / larynx morphogenesis / neural plate morphogenesis / mesodermal cell migration / type 2 fibroblast growth factor receptor binding / cell migration involved in mesendoderm migration / mitotic nuclear division / forebrain dorsal/ventral pattern formation / forebrain neuron development / dorsal/ventral axon guidance / Formation of the posterior neural plate / type 1 fibroblast growth factor receptor binding / regulation of odontogenesis of dentin-containing tooth / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / embryonic neurocranium morphogenesis / 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 / gonad development / cell proliferation in forebrain / aorta morphogenesis / epithelial to mesenchymal transition involved in endocardial cushion formation / 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 / bud elongation involved in lung branching / epidermis morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / mesonephros development / FGFR3b ligand binding and activation / reproductive structure development / limb bud formation / membranous septum morphogenesis / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / neuroepithelial cell differentiation / mesenchymal cell differentiation / forebrain morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of organ growth / Phospholipase C-mediated cascade; FGFR3 / branching involved in labyrinthine layer morphogenesis / mesenchymal cell proliferation involved in lung development / pyramidal neuron development / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / pharyngeal system development / regulation of osteoblast proliferation / positive regulation of G protein-coupled receptor signaling pathway / Phospholipase C-mediated cascade; FGFR4 / male genitalia development / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / embryonic pattern specification / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / outflow tract septum morphogenesis / dopaminergic neuron differentiation / metanephros development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / mesodermal cell differentiation / dorsal/ventral pattern formation / motor neuron axon guidance / bone morphogenesis / digestive tract development / signal transduction involved in regulation of gene expression
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 receptor 2 / Fibroblast growth factor 8 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMohammadi, M. / Olsen, S.K.
CitationJournal: Genes Dev. / Year: 2006
Title: Structural basis by which alternative splicing modulates the organizer activity of FGF8 in the brain
Authors: Olsen, S.K. / Li, J.Y.H. / Bromleigh, C. / Eliseenkova, A.V. / Ibrahimi, O.A. / Lao, Z. / Zhang, F. / Linhardt, R.J. / Joyner, A.L. / Mohammadi, M.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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
M: fibroblast growth factor 8 isoform B
P: Fibroblast growth factor receptor 2
N: fibroblast growth factor 8 isoform B
R: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)87,3304
Polymers87,3304
Non-polymers00
Water2,252125
1
M: fibroblast growth factor 8 isoform B
P: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)43,6652
Polymers43,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-11 kcal/mol
Surface area16110 Å2
MethodPISA
2
N: fibroblast growth factor 8 isoform B
R: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)43,6652
Polymers43,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-12 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.846, 46.908, 109.616
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere are two biological units. 1) chain A and chain B, and 2) chain C and chain D (i.e. two complexes of FGF8b with FGFR2c

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Components

#1: Protein fibroblast growth factor 8 isoform B / E.C.2.7.1.112 / FGF8b


Mass: 18906.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55075
#2: Protein Fibroblast growth factor receptor 2 / FGFR2c / FGFR-2 / Keratinocyte growth factor receptor 2 / CD332 antigen


Mass: 24758.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQH9, UniProt: P21802*PLUS, EC: 2.7.1.112
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18.5% mPEG 5000, 0.15M magnesium chloride, 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: 0.97925 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: Kohzu Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 44825 / Num. obs: 44825 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.084 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.8 % / Num. unique all: 4429 / Rsym value: 0.306 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EVT

1evt


Resolution: 2.28→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 6666 15.3 %random
Rwork0.2393 ---
all0.23931 43700 --
obs0.23931 43700 97.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.821 Å20 Å20.672 Å2
2--0.907 Å20 Å2
3---1.728 Å2
Refinement stepCycle: LAST / Resolution: 2.28→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 0 125 5345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006252
X-RAY DIFFRACTIONc_angle_deg1.3267
X-RAY DIFFRACTIONc_improper_angle_d0.77223
X-RAY DIFFRACTIONc_mcbond_it0.9471.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.4392
X-RAY DIFFRACTIONc_scangle_it2.1222.5

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