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- PDB-2ki4: FGF1-S100A13 complex structure: key component in non-classical pa... -

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Basic information

Entry
Database: PDB / ID: 2ki4
TitleFGF1-S100A13 complex structure: key component in non-classical path way of FGF1
Components
  • (Protein S100-A13) x 2
  • Heparin-binding growth factor 1
KeywordsPROTEIN TRANSPORT / acidic fibroblast growth factor / S100A13 / tetrameric complex / Acetylation / Alternative splicing / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism / Calcium
Function / homology
Function and homology information


mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of interleukin-1 alpha production / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / RAGE receptor binding / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of interleukin-1 alpha production / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / RAGE receptor binding / 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 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / 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 / positive regulation of hepatocyte proliferation / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / mast cell degranulation / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / fibroblast growth factor binding / positive regulation of intracellular signal transduction / 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 / activation of protein kinase B activity / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / neurogenesis / Signaling by FGFR2 in disease / positive regulation of endothelial cell migration / Signaling by FGFR1 in disease / positive regulation of MAP kinase activity / extracellular matrix / Hsp70 protein binding / regulation of cell migration / epithelial cell proliferation / positive regulation of cytokine production / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / lung development / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / positive regulation of cholesterol biosynthetic process / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / calcium-dependent protein binding / integrin binding / protein transport / PIP3 activates AKT signaling / heparin binding / cellular response to heat / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell cortex / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / copper ion binding / positive regulation of cell population proliferation / lipid binding / calcium ion binding / nucleolus / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Fibroblast growth factor 1 / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKrishna, S.M. / Rani, S.G. / Yu, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The heterohexameric complex structure, a component in the non-classical pathway for fibroblast growth factor 1 (FGF1) secretion.
Authors: Mohan, S.K. / Rani, S.G. / Yu, C.
History
DepositionApr 27, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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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: Protein S100-A13
C: Protein S100-A13
D: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)53,2134
Polymers53,2134
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 15118.044 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE)3 / References: UniProt: P05230
#2: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11488.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE)3 / References: UniProt: Q99584
#3: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11489.187 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE)3 / References: UniProt: Q99584
Has protein modificationN
Sequence detailsTHE CHAIN B AND C ARE S100A13 MONOMERS; BUT IN CHAIN B AND C THE 94, 97 AND 98 RESIDUES ARE ...THE CHAIN B AND C ARE S100A13 MONOMERS; BUT IN CHAIN B AND C THE 94, 97 AND 98 RESIDUES ARE DIFFERENT ISOMERS (DLY OR LYS).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: FGF1-S100A13 complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N] entity_1-1, 1.2 mM [U-100% 13C; U-100% 15N] entity_2-2, entity_3-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity_1-1[U-100% 13C; U-100% 15N]1
1.2 mMentity_2-2[U-100% 13C; U-100% 15N]1
1.2 mMentity_3-3[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2 & 2.2Linge, O'Donoghue and Nilgesstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ARIA/CNS HADDOCK
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 20 / Representative conformer: 1

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