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- PDB-1hkn: A complex between acidic fibroblast growth factor and 5-amino-2-n... -

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Basic information

Entry
Database: PDB / ID: 1hkn
TitleA complex between acidic fibroblast growth factor and 5-amino-2-naphthalenesulfonate
ComponentsHEPARIN-BINDING GROWTH FACTOR 1
KeywordsGROWTH FACTOR / MITOGEN / ANGIOGENESIS / HEPARIN-BINDING
Function / homology
Function and homology information


mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / 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 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / S100 protein binding / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / positive regulation of MAP kinase activity / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / activation of protein kinase B activity / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / neurogenesis / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / extracellular matrix / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / growth factor activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / wound healing / positive regulation of cholesterol biosynthetic process / integrin binding / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heparin binding / cellular response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell cortex / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Mainly Beta
Similarity search - Domain/homology
5-AMINO-NAPHTALENE-2-MONOSULFONATE / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFernandez-Tornero, C. / Lozano, R.M. / Gimenez-Gallego, G. / Romero, A.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Leads for Development of New Naphthalenesulfonate Derivatives with Enhanced Antiangiogenic Activity: Crystal Structure of Acidic Fibroblast Growth Factor in Complex with 5-Amino-2-Naphthalenesulfonate
Authors: Fernandez-Tornero, C. / Lozano, R.M. / Redondo-Horcajo, M. / Gomez, A. / Lopez, J. / Quesada, E. / Uriel, C. / Valverde, S. / Cuevas, P. / Romero, A. / Gimenez-Gallego, G.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Solution Structure of Acidic Fibroblast Growth Factor Bound to 1,3,6-Naphthalenetrisulfonate: A Minimal Model for the Anti-Tumoral Action of Suramins and Suradistas
Authors: Lozano, M.R. / Jimenez, M. / Santoro, J. / Rico, M. / Gimenez-Gallego, G.
#2: Journal: Eur.J.Biochem. / Year: 1996
Title: X-Ray Structure of Native Full-Length Human Fibroblast-Growth Factor at 0.25 Nm Resolution
Authors: Romero, A. / Pineda-Lucena, A. / Gimenez-Gallego, G.
History
DepositionMar 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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: HEPARIN-BINDING GROWTH FACTOR 1
D: HEPARIN-BINDING GROWTH FACTOR 1
E: HEPARIN-BINDING GROWTH FACTOR 1
F: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7118
Polymers94,2646
Non-polymers4462
Water1,856103
1
A: HEPARIN-BINDING GROWTH FACTOR 1


Theoretical massNumber of molelcules
Total (without water)15,7111
Polymers15,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEPARIN-BINDING GROWTH FACTOR 1


Theoretical massNumber of molelcules
Total (without water)15,7111
Polymers15,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9342
Polymers15,7111
Non-polymers2231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9342
Polymers15,7111
Non-polymers2231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: HEPARIN-BINDING GROWTH FACTOR 1


Theoretical massNumber of molelcules
Total (without water)15,7111
Polymers15,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: HEPARIN-BINDING GROWTH FACTOR 1


Theoretical massNumber of molelcules
Total (without water)15,7111
Polymers15,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.530, 47.210, 97.840
Angle α, β, γ (deg.)90.00, 107.04, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99901, 0.03623, -0.02565), (-0.03644, 0.99931, -0.00765), (0.02535, 0.00858, 0.99964)-31.41383, -21.24867, -46.92897
2given(-0.86352, -0.33466, -0.37727), (-0.34267, -0.1595, 0.92582), (-0.37001, 0.92874, 0.02306)52.53755, -55.80906, 21.5929
3given(-0.83063, -0.32127, -0.4548), (-0.44103, -0.11904, 0.88956), (-0.33993, 0.93947, -0.04281)0.58795, -28.6458, 34.42809
4given(0.79235, 0.22686, 0.56632), (0.03473, -0.94356, 0.32938), (0.60908, -0.24131, -0.75551)-61.07424, -11.97428, 73.12293
5given(0.78459, 0.23728, 0.57281), (0.03471, -0.93923, 0.34153), (0.61904, -0.24808, -0.74515)3.75493, -18.20288, 52.61682

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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: 15710.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05230
#2: Chemical ChemComp-N2M / 5-AMINO-NAPHTALENE-2-MONOSULFONATE


Mass: 223.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.03 Å3/Da / Density % sol: 39.1 %
Crystal growpH: 7.8
Details: CRYSTALS OF THE COMPLEX BETWEEN AFGF AND 5-AMINO-2-NMS WERE GROWN BY MIXING 0.75 MM PROTEIN, 1.5 MM OF THE INHIBITOR AND 60% SODIUM/PO, pH 7.80
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.85 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.75 mMprotein1drop
21.5 mMinhibitor1drop
360 %sodium potassium tartrate1drop
45 mMsodium phosphate1droppH7.85
51.3 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9073 Å / Relative weight: 1
ReflectionResolution: 2→33.5 Å / Num. obs: 56957 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.4 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 33.5 Å / Num. measured all: 321819 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: PDB ENTRY 2AXM

2axm


Resolution: 2→33.57 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1758636.06 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT PHE1001-LYS1009, PHE2001-LYS2009, PHE3001-TYR3008, PHE4001-LYS4009, PHE5001-TYR5008, PHE6001- LYS6009 SEVERAL RESIDUES AT THE C- ...Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT PHE1001-LYS1009, PHE2001-LYS2009, PHE3001-TYR3008, PHE4001-LYS4009, PHE5001-TYR5008, PHE6001- LYS6009 SEVERAL RESIDUES AT THE C-TERMINAL WERE NOT MODELLED SER1138-ASP1140, SER2138-ASP2140, SER3138-ASP3140, SER1139- ASP4140, SER5139-ASP5140, SER6138-ASP6140
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5786 10.2 %RANDOM
Rwork0.228 ---
obs0.228 56957 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5897 Å2 / ksol: 0.387043 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å20 Å25.56 Å2
2--2.18 Å20 Å2
3----7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6168 0 30 103 6301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 949 10 %
Rwork0.27 8582 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION35NN2MS.PARAM5NN2MS.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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