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- PDB-1qql: THE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 7/1 CHIMERA -

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Basic information

Entry
Database: PDB / ID: 1qql
TitleTHE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 7/1 CHIMERA
ComponentsFibroblast growth factor 7, Fibroblast growth factor 1 chimera
KeywordsHORMONE/GROWTH FACTOR / BETA-TREFOIL / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


secretion by lung epithelial cell involved in lung growth / FGFR2b ligand binding and activation / type 2 fibroblast growth factor receptor binding / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / positive regulation of keratinocyte proliferation ...secretion by lung epithelial cell involved in lung growth / FGFR2b ligand binding and activation / type 2 fibroblast growth factor receptor binding / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / positive regulation of keratinocyte proliferation / Negative regulation of FGFR2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / positive regulation of myoblast proliferation / regulation of endothelial cell chemotaxis to fibroblast growth factor / phosphatidylcholine biosynthetic process / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / phospholipid biosynthetic process / positive regulation of keratinocyte migration / FGFR2b ligand binding and activation / mesenchymal cell proliferation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / organ induction / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / regulation of synapse maturation / surfactant homeostasis / protein localization to cell surface / S100 protein binding / positive regulation of hepatocyte proliferation / RAF/MAP kinase cascade / myoblast proliferation / endothelial cell proliferation / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / hair follicle morphogenesis / PI-3K cascade:FGFR3 / positive chemotaxis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / chemoattractant activity / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / GABA-ergic synapse / ovarian follicle development / 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 / positive regulation of endothelial cell proliferation / Signaling by FGFR1 in disease / Hsp70 protein binding / regulation of cell migration / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / positive regulation of epithelial cell proliferation / epithelial cell proliferation / animal organ morphogenesis / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / lung development / Negative regulation of FGFR1 signaling / positive regulation of MAP kinase activity / growth factor activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / PIP3 activates AKT signaling / heparin binding
Similarity search - Function
HBGF/FGF family signature. / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1 / Fibroblast growth factor 7 / Fibroblast growth factor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsYe, S. / Luo, Y. / Pelletier, H. / McKeehan, W.L.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural basis for interaction of FGF-1, FGF-2, and FGF-7 with different heparan sulfate motifs.
Authors: Ye, S. / Luo, Y. / Lu, W. / Jones, R.B. / Linhardt, R.J. / Capila, I. / Toida, T. / Kan, M. / Pelletier, H. / McKeehan, W.L.
#1: Journal: Biochemistry / Year: 1998
Title: The glycine box: a determinant of specificity for fibroblast growth factor.
Authors: Luo, Y. / Lu, W. / Mohamedali, K.A. / Jang, J.H. / Jones, R.B. / Gabriel, J.L. / Kan, M. / McKeehan, W.L.
#2: Journal: Science / Year: 1989
Title: Human KGF is FGF-related with properties of a paracrine effector of epithelial cell growth.
Authors: Finch, P.W. / Rubin, J.S. / Miki, T. / Ron, D. / Aaronson, S.A.
#3: Journal: Nature / Year: 1998
Title: Structure of a heparin-linked biologically active dimer of fibroblast growth factor.
Authors: DiGabriele, A.D. / Lax, I. / Chen, D.I. / Svahn, C.M. / Jaye, M. / Schlessinger, J. / Hendrickson, W.A.
#4: Journal: Science / Year: 1996
Title: Heparin structure and interactions with basic fibroblast growth factor.
Authors: Faham, S. / Hileman, R.E. / Fromm, J.R. / Linhardt, R.J. / Rees, D.C.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 2, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 7, Fibroblast growth factor 1 chimera


Theoretical massNumber of molelcules
Total (without water)16,4341
Polymers16,4341
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.8, 89.8, 65.5
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Fibroblast growth factor 7, Fibroblast growth factor 1 chimera / FGF / FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / ...FGF / FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin-binding growth factor 1 / HBGF-1


Mass: 16433.945 Da / Num. of mol.: 1
Fragment: DUAL-FUNCTION CHIMERA BETWEEN RAT FGF-7 ENCODED BY EXON 1 AND 2 AND HUMAN FGF-1 ENCODED BY EXON 3,DUAL-FUNCTION CHIMERA BETWEEN RAT FGF-7 ENCODED BY EXON 1 AND 2 AND HUMAN FGF-1 ENCODED BY EXON 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human)
Genus: Rattus, Homo / Species: , / Strain: , / Description: NONE / Gene: Fgf7, FGF1, FGFA / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q9ERN5, UniProt: P05230, UniProt: Q02195*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SODIUM PHOSPHATE, POTASSIUM PHOSPHATE, SODIUM SULPHATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMHEPES1droppH7.0
320 mMammonium sulfate1drop
410 mMdithiothreitol1drop
50.2 mMEDTA1drop
61.75 Msodium potassium phosphate1reservoirpH7.0
720 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1991
21
31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS F210.9794
SYNCHROTRONCHESS F220.9792
SYNCHROTRONCHESS F230.9639
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 31, 1998
2
3
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97921
30.96391
ReflectionResolution: 2.3→30 Å / Num. all: 7140 / Num. obs: 7140 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 28.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.299 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 64157
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→6 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.328 623 -RANDOM
Rwork0.237 ---
all0.262 6863 --
obs0.246 6024 87.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 0 159 1241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS

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