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- PDB-2m49: Structural Insights into Human S100B and Basic Fibroblast Growth ... -

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Basic information

Entry
Database: PDB / ID: 2m49
TitleStructural Insights into Human S100B and Basic Fibroblast Growth Factor (FGF2) Interaction
Components
  • Fibroblast growth factor 2Basic fibroblast growth factor
  • Protein S100-B
KeywordsCYTOKINE/METAL BINDING PROTEIN / S100B / FGF2 / CYTOKINE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of fibroblast growth factor receptor signaling pathway / adaptive thermogenesis / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / sympathetic neuron projection extension / cerebellar granule cell precursor proliferation / positive regulation of stem cell differentiation / positive regulation of epithelial tube formation / hyaluronan catabolic process / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / glial cell differentiation / negative regulation of wound healing / inner ear auditory receptor cell differentiation / stem cell development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / RAGE receptor binding / angiogenesis involved in coronary vascular morphogenesis / 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 / mammary gland epithelial cell differentiation / 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 / paracrine signaling / ion binding / negative regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / S100 protein binding / embryo development ending in birth or egg hatching / endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / Signaling by FGFR2 IIIa TM / positive regulation of DNA biosynthetic process / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR3 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / positive regulation of stem cell proliferation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / regulation of neuronal synaptic plasticity / chemoattractant activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of cell division / negative regulation of blood vessel endothelial cell migration / Non-integrin membrane-ECM interactions / PI3K Cascade / neuroblast proliferation / response to axon injury / canonical Wnt signaling pathway / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / regulation of angiogenesis / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / Nuclear signaling by ERBB4 / release of sequestered calcium ion into cytosol / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling
Similarity search - Function
Protein S100-B / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain ...Protein S100-B / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / 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, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein S100-B / Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsGupta, A.A. / Yu, C.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling
Authors: Gupta, A.A. / Chou, R.H. / Li, H. / Yang, L.W. / Yu, C.
History
DepositionFeb 3, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 2
B: Protein S100-B
D: Protein S100-B
C: Fibroblast growth factor 2


Theoretical massNumber of molelcules
Total (without water)50,0374
Polymers50,0374
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fibroblast growth factor 2 / Basic fibroblast growth factor / FGF-2 / Basic fibroblast growth factor / bFGF / Heparin-binding growth factor 2 / HBGF-2


Mass: 14422.525 Da / Num. of mol.: 2 / Fragment: UNP residues 161-286 / Mutation: C211S, C229S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09038
#2: Protein Protein S100-B / S-100 protein beta chain / S-100 protein subunit beta / S100 calcium-binding protein B


Mass: 10595.841 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Human S100B and Basic Fibroblast Growth Factor (FGF2) Interaction
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HNCO
1513D HCACO
1613D CBCA(CO)NH
1713D HN(CA)CB

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Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N] S100B-1, 20 mM TRIS-2, 50 mM ammonium sulfate-3, 5 mM calcium chloride-4, 5 mM DTT-5, 0.01 % sodium azide-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMS100B-1[U-100% 13C; U-100% 15N]1
20 mMTRIS-21
50 mMammonium sulfate-31
5 mMcalcium chloride-41
5 mMDTT-51
0.01 %sodium azide-61
Sample conditionsIonic strength: 0.050 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ3.2Variancollection
VnmrJ3.2Varianprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
HADDOCKAlexandre Bonvinstructure solution
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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