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- PDB-1g82: STRUCTURE OF FIBROBLAST GROWTH FACTOR 9 -

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Basic information

Entry
Database: PDB / ID: 1g82
TitleSTRUCTURE OF FIBROBLAST GROWTH FACTOR 9
ComponentsFIBROBLAST GROWTH FACTOR 9
KeywordsHORMONE/GROWTH FACTOR / Fibroblast Growth Factor / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / positive regulation of reproductive process / Sertoli cell proliferation / Transcriptional regulation of testis differentiation / embryonic skeletal system development / FGFR3b ligand binding and activation / eye development / Signaling by activated point mutants of FGFR3 ...regulation of timing of cell differentiation / positive regulation of activin receptor signaling pathway / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / positive regulation of reproductive process / Sertoli cell proliferation / Transcriptional regulation of testis differentiation / embryonic skeletal system development / FGFR3b ligand binding and activation / eye development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / embryonic digestive tract development / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation / 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 / Phospholipase C-mediated cascade; FGFR4 / male sex determination / activin receptor signaling pathway / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / lung-associated mesenchyme development / positive regulation of smoothened signaling pathway / positive regulation of vascular associated smooth muscle cell migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / embryonic limb morphogenesis / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / smoothened signaling pathway / inner ear morphogenesis / PI-3K cascade:FGFR3 / negative regulation of Wnt signaling pathway / PI-3K cascade:FGFR2 / positive regulation of stem cell proliferation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / canonical Wnt signaling pathway / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / vascular endothelial growth factor receptor signaling pathway / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / regulation of cell migration / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / substantia nigra development / Signaling by FGFR1 in disease / stem cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / animal organ morphogenesis / growth factor activity / lung development / osteoblast differentiation / protein import into nucleus / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / positive regulation of canonical Wnt signaling pathway / PIP3 activates AKT signaling / cell-cell signaling / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell differentiation / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular region / 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
: / Fibroblast growth factor 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHecht, H.J. / Adar, R. / Hofmann, B. / Bogin, O. / Weich, H. / Yayon, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of fibroblast growth factor 9 shows a symmetric dimer with unique receptor- and heparin-binding interfaces.
Authors: Hecht, H.J. / Adar, R. / Hofmann, B. / Bogin, O. / Weich, H. / Yayon, A.
History
DepositionNov 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR 9
B: FIBROBLAST GROWTH FACTOR 9
C: FIBROBLAST GROWTH FACTOR 9
D: FIBROBLAST GROWTH FACTOR 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,54220
Polymers74,4564
Non-polymers3,08616
Water2,648147
1
A: FIBROBLAST GROWTH FACTOR 9
D: FIBROBLAST GROWTH FACTOR 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,94610
Polymers37,2282
Non-polymers1,7178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-49 kcal/mol
Surface area15660 Å2
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR 9
C: FIBROBLAST GROWTH FACTOR 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59610
Polymers37,2282
Non-polymers1,3688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-69 kcal/mol
Surface area15850 Å2
MethodPISA
3
A: FIBROBLAST GROWTH FACTOR 9
D: FIBROBLAST GROWTH FACTOR 9
hetero molecules

B: FIBROBLAST GROWTH FACTOR 9
C: FIBROBLAST GROWTH FACTOR 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,54220
Polymers74,4564
Non-polymers3,08616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_654-y+3/2,x,z-1/41
Buried area9700 Å2
ΔGint-119 kcal/mol
Surface area30870 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-117 kcal/mol
Surface area30810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.947, 151.947, 117.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Detailsthe biological assembly is a dimer. The asymmetric unit contains two dimers. The dimers are formed by molecule A and D, and B and C.

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Components

#1: Protein
FIBROBLAST GROWTH FACTOR 9 /


Mass: 18614.072 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBACPAK9 / Cell line (production host): SF9 / Production host: unidentified baculovirus / References: PIR: A48137, UniProt: P31371*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(2+?)][]{[(?+2)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 4.54 Å3/Da / Density % sol: 72.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: Ammonium sulfate, MES, TRIS, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.1 mg/mlprotein1drop
22.0 Mammonium sulfate1drop
30.1 MMES/Tris1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 22, 1998 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.6→39.5 Å / Num. all: 40985 / Num. obs: 40985 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 68.211 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.052 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5971 / Rsym value: 0.222 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
EPMRphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AFG

2afg


Resolution: 2.6→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2058 5 %RANDOM
Rwork0.2083 ---
all0.2103 40985 --
obs0.2103 38917 99.9 %-
Displacement parametersBiso mean: 51.97 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24693 Å-
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5145 0 188 147 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0340.021
X-RAY DIFFRACTIONp_mcbond_it1.3891.5
X-RAY DIFFRACTIONp_mcangle_it2.5582
X-RAY DIFFRACTIONp_scbond_it3.7283
X-RAY DIFFRACTIONp_scangle_it6.0094.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 2.7

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