[English] 日本語
Yorodumi
- PDB-2m49: Structural Insights into Human S100B and Basic Fibroblast Growth ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m49
TitleStructural Insights into Human S100B and Basic Fibroblast Growth Factor (FGF2) Interaction
Components
  • Fibroblast growth factor 2
  • 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 lens fiber cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of lens fiber cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / 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 / chemokine binding / chondroblast differentiation / lymphatic endothelial cell migration / 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 / Formation of the nephric duct / receptor-receptor interaction / FGFR2b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / paracrine signaling / hyaluronan catabolic process / inner ear auditory receptor cell differentiation / glial cell differentiation / negative regulation of wound healing / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / RAGE receptor binding / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / stem cell development / Phospholipase C-mediated cascade; FGFR3 / embryonic morphogenesis / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / 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 / organ induction / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / 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 / Signaling by FGFR2 IIIa TM / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / chemoattractant activity / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / positive regulation of cell division / negative regulation of blood vessel endothelial cell migration / Advanced glycosylation endproduct receptor signaling / PI3K Cascade / Non-integrin membrane-ECM interactions / neuroblast proliferation / fibroblast growth factor receptor signaling pathway / response to axon injury / positive regulation of blood vessel endothelial cell migration / canonical Wnt signaling pathway / regulation of angiogenesis / SHC-mediated cascade:FGFR2 / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / positive regulation of cardiac muscle cell proliferation / Nuclear signaling by ERBB4 / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / FRS-mediated FGFR4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

#1: Protein Fibroblast growth factor 2 / 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

-
Experimental details

-
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

-
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: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more