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- PDB-1djs: LIGAND-BINDING PORTION OF FIBROBLAST GROWTH FACTOR RECEPTOR 2 IN ... -

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Basic information

Entry
Database: PDB / ID: 1djs
TitleLIGAND-BINDING PORTION OF FIBROBLAST GROWTH FACTOR RECEPTOR 2 IN COMPLEX WITH FGF1
Components
  • PROTEIN (FIBROBLAST GROWTH FACTOR 1)
  • PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
KeywordsHORMONE/GROWTH FACTOR/RECEPTOR / FGFR / FGF / IMMUNOGLOBULIN / IMMUNE SYSTEM / HORMONE-GROWTH FACTOR-RECEPTOR 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 / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / reproductive structure development / limb bud formation / membranous septum morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / lung lobe 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 / epithelial cell proliferation involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / 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 / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / regulation of osteoblast proliferation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / 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 / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / mesodermal cell differentiation / bone morphogenesis / S100 protein binding / positive regulation of hepatocyte proliferation / digestive tract development / skeletal system morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / inner ear morphogenesis / organ growth / hair follicle morphogenesis / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / ventricular cardiac muscle tissue morphogenesis / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of osteoblast differentiation / PI-3K cascade:FGFR2 / lung alveolus development / PI-3K cascade:FGFR4 / prostate epithelial cord elongation / PI-3K cascade:FGFR1 / midbrain development / positive regulation of sprouting angiogenesis / bone mineralization / fibroblast growth factor binding / positive regulation of intracellular signal transduction / positive regulation of cell division / excitatory synapse / PI3K Cascade / positive regulation of Wnt signaling pathway / anatomical structure morphogenesis / cell fate commitment
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 / MAD / Resolution: 2.4 Å
AuthorsStauber, D.J. / Digabriele, A.D. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structural interactions of fibroblast growth factor receptor with its ligands.
Authors: Stauber, D.J. / DiGabriele, A.D. / Hendrickson, W.A.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,50011
Polymers39,6352
Non-polymers8659
Water5,747319
1
A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules

A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,99922
Polymers79,2704
Non-polymers1,72918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area12010 Å2
ΔGint-301 kcal/mol
Surface area30810 Å2
MethodPISA
2
A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules

A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules

A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules

A: PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)
B: PROTEIN (FIBROBLAST GROWTH FACTOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,99844
Polymers158,5408
Non-polymers3,45836
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area28610 Å2
ΔGint-649 kcal/mol
Surface area57040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.970, 129.970, 129.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein PROTEIN (FIBROBLAST GROWTH FACTOR RECEPTOR 2)


Mass: 24298.936 Da / Num. of mol.: 1 / Fragment: IG-LIKE DOMAINS 2 AND 3 / Mutation: N147T,S148L,N149E,N150P,K151E,R152G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P21802, EC: 2.7.1.112
#2: Protein PROTEIN (FIBROBLAST GROWTH FACTOR 1)


Mass: 15336.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growpH: 7.5 / Details: 1.6M AMMONIUM SULFATE, 10MM TRIS (PH7.5), pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
31.6 Mammonium sulfate1reservoir
410 mMTris-HCl1reservoir
2reservoir solution1dropsame volume of 2:1 diluted reservoir solution

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9919, 0.9793, 0.9791, 0.9641
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 17, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99191
20.97931
30.97911
40.96411
ReflectionResolution: 2.4→20 Å / Num. obs: 41549 / % possible obs: 99.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.402 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 180297
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→6 Å / SU B: 5.181 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1040 5 %RANDOM
Rwork0.221 ---
obs0.227 19354 --
Displacement parametersBiso mean: 29.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 45 319 3066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d2.3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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