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S100B (S100 calcium binding protein B)

Written2007-05M Rosario Fernandez-Fernandez, Alan R Fersht
Centre for Protein Engineering, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom

(Note : for Links provided by Atlas : click)

Identity

Alias_namesS100 calcium binding protein
Alias_symbol (synonym)S100beta
Other aliasNEF
S100
S100Beta
HGNC (Hugo) S100B
LocusID (NCBI) 6285
Atlas_Id 42195
Location 21q22.3  [Link to chromosome band 21q22]
Location_base_pair Starts at 46598618 and ends at 46605122 bp from pter ( according to hg19-Feb_2009)  [Mapping S100B.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
HDAC3 (5q31.3) / S100B (21q22.3)JUND (19p13.11) / S100B (21q22.3)RUBCN (3q29) / S100B (21q22.3)
S100B (21q22.3) / TCTN1 (12q24.11)

DNA/RNA

Description The gene encompasses 17.3 Kb of DNA; 3 exons (the first one contains the 5' untranslated region).
Transcription 1135 b mRNA; 279 b coding sequence.

Protein

Description 92 amino acids (including initial methionine that is generally processed in vivo);
10.5 kDa monomer (S100B can form homodimers and heterodimers with other proteins of the S100 family, described for S100A1).
Expression S100B highest levels are found in brain. The protein is primarily found in astrocytes. Outside the central nervous system it can be found in chondrocytes and melanocytes.
Localisation Nuclear and cytoplasmic. It has both intracellular and extracellular roles.
Function The exact function of S100B is not fully understood. It inhibits microtubule assembly, has been involved in the regulation of cell cycle progression and differentiation and is able to induce neurite extension. This latest effect seems to be dependent on the concentration of S100B and occurs at nanomolar concentrations.
But micromolar levels of extracellular S100B stimulate apoptosis in vitro. Calcium binding induces a conformational change in S100B that allows the interaction with a variety of target proteins. These include p53 tumour suppressor, the microtubule-associated protein tau, the cytoskeletal protein tubulin (and its prokaryotic ancestor FtsZ), the scaffold protein IQGAP1, the intermediate filament protein glial fibrillary acidic protein (GFAP),the actin capping protein CapZ and the giant phosphoprotein AHNAK. Over-expression of S100B has been proposed to play a role in different neuro-pathologies.
Homology S100B belongs to the S100 family of calcium binding proteins, a highly homologous family. These proteins contain two EF-hand calcium binding domains. The S100 genes are present exclusively in vertebrates.

Mutations

Note Have not been reported.

Implicated in

Note
Disease Overexpression of S100B has been generally linked to neurodegeneration. It is over-expressed in the brain of patients suffering from Alzheimer's disease, epilepsy or amyotrophic lateral sclerosis. The gene coding for S100B maps in the Down's syndrome region of chromosome 21, and its over-expression, due to the trisomic state, may be responsible for the neurological disturbances in Down's syndrome.
Oncogenesis S100B may be involved in the proliferation of melanoma cells. It has been shown to be elevated in primary malignant melanomas. However, S100B is used as a predictor of survival prognosis as elevated levels of S100B in serum are associated with the survival rate.
  

Bibliography

Gene encoding the beta subunit of S100 protein is on chromosome 21: implications for Down syndrome.
Allore R, O'Hanlon D, Price R, Neilson K, Willard HF, Cox DR, Marks A, Dunn RJ
Science (New York, N.Y.). 1988 ; 239 (4845) : 1311-1313.
PMID 2964086
 
The Ca2+-binding sequence in bovine brain S100b protein beta-subunit. A spectroscopic study.
Baudier J, Cole RD
The Biochemical journal. 1989 ; 264 (1) : 79-85.
PMID 2604719
 
Characterization of the tumor suppressor protein p53 as a protein kinase C substrate and a S100b-binding protein.
Baudier J, Delphin C, Grunwald D, Khochbin S, Lawrence JJ
Proceedings of the National Academy of Sciences of the United States of America. 1992 ; 89 (23) : 11627-11631.
PMID 1454855
 
Ions binding to S100 proteins: structural changes induced by calcium and zinc on S100a and S100b proteins.
Baudier J, Gérard D
Biochemistry. 1983 ; 22 (14) : 3360-3369.
PMID 6615778
 
Comparison of S100b protein with calmodulin: interactions with melittin and microtubule-associated tau proteins and inhibition of phosphorylation of tau proteins by protein kinase C.
Baudier J, Mochly-Rosen D, Newton A, Lee SH, Koshland DE Jr, Cole RD
Biochemistry. 1987 ; 26 (10) : 2886-2893.
PMID 3111527
 
Calcium-dependent interaction of S100B with the C-terminal domain of the tumor suppressor p53.
Delphin C, Ronjat M, Deloulme JC, Garin G, Debussche L, Higashimoto Y, Sakaguchi K, Baudier J
The Journal of biological chemistry. 1999 ; 274 (15) : 10539-10544.
PMID 10187847
 
Solution structure of rat apo-S100B(beta beta) as determined by NMR spectroscopy.
Drohat AC, Amburgey JC, Abildgaard F, Starich MR, Baldisseri D, Weber DJ
Biochemistry. 1996 ; 35 (36) : 11577-11588.
PMID 8794737
 
Solution structure of calcium-bound rat S100B(betabeta) as determined by nuclear magnetic resonance spectroscopy,.
Drohat AC, Baldisseri DM, Rustandi RR, Weber DJ
Biochemistry. 1998 ; 37 (9) : 2729-2740.
PMID 9485423
 
Proteins of the S100 family regulate the oligomerization of p53 tumor suppressor.
Fernandez-Fernandez MR, Veprintsev DB, Fersht AR
Proceedings of the National Academy of Sciences of the United States of America. 2005 ; 102 (13) : 4735-4740.
PMID 15781852
 
Expression of S100B during embryonic development of the mouse cerebellum.
Hachem S, Laurenson AS, Hugnot JP, Legraverend C
BMC developmental biology. 2007 ; 7 : page 17.
PMID 17362503
 
S100B protein, 5-S-cysteinyldopa and 6-hydroxy-5-methoxyindole-2-carboxylic acid as biochemical markers for survival prognosis in patients with malignant melanoma.
Kärnell R, von Schoultz E, Hansson LO, Nilsson B, Arstrand K, Kågedal B
Melanoma research. 1997 ; 7 (5) : 393-399.
PMID 9429222
 
Identification of the binding site on S100B protein for the actin capping protein CapZ.
Kilby PM, Van Eldik LJ, Roberts GC
Protein science : a publication of the Protein Society. 1997 ; 6 (12) : 2494-2503.
PMID 9416599
 
S100B-induced microglial and neuronal IL-1 expression is mediated by cell type-specific transcription factors.
Liu L, Li Y, Van Eldik LJ, Griffin WS, Barger SW
Journal of neurochemistry. 2005 ; 92 (3) : 546-553.
PMID 15659225
 
Calcium-dependent interaction of S100b, troponin C, and calmodulin with an immobilized phenothiazine.
Marshak DR, Watterson DM, Van Eldik LJ
Proceedings of the National Academy of Sciences of the United States of America. 1981 ; 78 (11) : 6793-6797.
PMID 6947252
 
Calcium regulation of Ndr protein kinase mediated by S100 calcium-binding proteins.
Millward TA, Heizmann CW, Schäfer BW, Hemmings BA
The EMBO journal. 1998 ; 17 (20) : 5913-5922.
PMID 9774336
 
Glial protein S100B modulates long-term neuronal synaptic plasticity.
Nishiyama H, Knopfel T, Endo S, Itohara S
Proceedings of the National Academy of Sciences of the United States of America. 2002 ; 99 (6) : 4037-4042.
PMID 11891290
 
Key role of Src kinase in S100B-induced activation of the receptor for advanced glycation end products in vascular smooth muscle cells.
Reddy MA, Li SL, Sahar S, Kim YS, Xu ZG, Lanting L, Natarajan R
The Journal of biological chemistry. 2006 ; 281 (19) : 13685-13693.
PMID 16551628
 
Astrocytosis and axonal proliferation in the hippocampus of S100b transgenic mice.
Reeves RH, Yao J, Crowley MR, Buck S, Zhang X, Yarowsky P, Gearhart JD, Hilt DC
Proceedings of the National Academy of Sciences of the United States of America. 1994 ; 91 (12) : 5359-5363.
PMID 8202493
 
Structure of the negative regulatory domain of p53 bound to S100B(betabeta).
Rustandi RR, Baldisseri DM, Weber DJ
Nature structural biology. 2000 ; 7 (7) : 570-574.
PMID 10876243
 
Concerted regulation of wild-type p53 nuclear accumulation and activation by S100B and calcium-dependent protein kinase C.
Scotto C, Delphin C, Deloulme JC, Baudier J
Molecular and cellular biology. 1999 ; 19 (10) : 7168-7180.
PMID 10490652
 
Association of S100B with intermediate filaments and microtubules in glial cells.
Sorci G, Agneletti AL, Bianchi R, Donato R
Biochimica et biophysica acta. 1998 ; 1448 (2) : 277-289.
PMID 9920418
 
S100B inhibits myogenic differentiation and myotube formation in a RAGE-independent manner.
Sorci G, Riuzzi F, Agneletti AL, Marchetti C, Donato R
Molecular and cellular biology. 2003 ; 23 (14) : 4870-4881.
PMID 12832473
 
Evidence for a wide extra-astrocytic distribution of S100B in human brain.
Steiner J, Bernstein HG, Bielau H, Berndt A, Brisch R, Mawrin C, Keilhoff G, Bogerts B
BMC neuroscience. 2007 ; 8 : page 2.
PMID 17199889
 

Citation

This paper should be referenced as such :
Fernandez-Fernandez, M Rosario ; Fersht, Alan R
S100B (S100 calcium binding protein B)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(4):314-315.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/S100BID42195ch21q22.html


External links

Nomenclature
HGNC (Hugo)S100B   10500
Cards
AtlasS100BID42195ch21q22
Entrez_Gene (NCBI)S100B  6285  S100 calcium binding protein B
AliasesNEF; S100; S100-B; S100beta
GeneCards (Weizmann)S100B
Ensembl hg19 (Hinxton)ENSG00000160307 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000160307 [Gene_View]  chr21:46598618-46605122 [Contig_View]  S100B [Vega]
ICGC DataPortalENSG00000160307
TCGA cBioPortalS100B
AceView (NCBI)S100B
Genatlas (Paris)S100B
WikiGenes6285
SOURCE (Princeton)S100B
Genetics Home Reference (NIH)S100B
Genomic and cartography
GoldenPath hg38 (UCSC)S100B  -     chr21:46598618-46605122 -  21q22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)S100B  -     21q22.3   [Description]    (hg19-Feb_2009)
EnsemblS100B - 21q22.3 [CytoView hg19]  S100B - 21q22.3 [CytoView hg38]
Mapping of homologs : NCBIS100B [Mapview hg19]  S100B [Mapview hg38]
OMIM176990   
Gene and transcription
Genbank (Entrez)AA310307 BC001766 BC041935 CR542123 DQ892491
RefSeq transcript (Entrez)NM_006272
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)S100B
Cluster EST : UnigeneHs.422181 [ NCBI ]
CGAP (NCI)Hs.422181
Alternative Splicing GalleryENSG00000160307
Gene ExpressionS100B [ NCBI-GEO ]   S100B [ EBI - ARRAY_EXPRESS ]   S100B [ SEEK ]   S100B [ MEM ]
Gene Expression Viewer (FireBrowse)S100B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6285
GTEX Portal (Tissue expression)S100B
Human Protein AtlasENSG00000160307-S100B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP04271   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP04271  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP04271
Splice isoforms : SwissVarP04271
PhosPhoSitePlusP04271
Domaine pattern : Prosite (Expaxy)EF_HAND_1 (PS00018)    EF_HAND_2 (PS50222)    S100_CABP (PS00303)   
Domains : Interpro (EBI)EF-hand-dom_pair    EF_Hand_1_Ca_BS    EF_hand_dom    S100-B    S100/CaBP-9k_CS    S100_Ca-bd_sub   
Domain families : Pfam (Sanger)EF-hand_1 (PF00036)    S_100 (PF01023)   
Domain families : Pfam (NCBI)pfam00036    pfam01023   
Domain families : Smart (EMBL)EFh (SM00054)  S_100 (SM01394)  
Conserved Domain (NCBI)S100B
DMDM Disease mutations6285
Blocks (Seattle)S100B
PDB (SRS)1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
PDB (PDBSum)1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
PDB (IMB)1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
PDB (RSDB)1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
Structural Biology KnowledgeBase1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
SCOP (Structural Classification of Proteins)1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
CATH (Classification of proteins structures)1MQ1    1UWO    2H61    2M49    2PRU    3CZT    3D0Y    3D10    3HCM    4XYN    5CSF    5CSI    5CSJ    5CSN    5D7F   
SuperfamilyP04271
Human Protein Atlas [tissue]ENSG00000160307-S100B [tissue]
Peptide AtlasP04271
HPRD01505
IPIIPI00299399   IPI00797361   
Protein Interaction databases
DIP (DOE-UCLA)P04271
IntAct (EBI)P04271
FunCoupENSG00000160307
BioGRIDS100B
STRING (EMBL)S100B
ZODIACS100B
Ontologies - Pathways
QuickGOP04271
Ontology : AmiGOruffle  calcium ion binding  protein binding  extracellular region  extracellular space  nucleus  cytoplasm  cytoplasm  axonogenesis  central nervous system development  learning or memory  memory  zinc ion binding  cell proliferation  positive regulation of cell proliferation  regulation of cell shape  identical protein binding  protein homodimerization activity  protein homodimerization activity  neuronal cell body  positive regulation of apoptotic process  positive regulation of I-kappaB kinase/NF-kappaB signaling  S100 protein binding  innate immune response  tau protein binding  regulation of neuronal synaptic plasticity  calcium-dependent protein binding  perinuclear region of cytoplasm  astrocyte differentiation  RAGE receptor binding  response to glucocorticoid  response to methylmercury  long-term synaptic potentiation  cellular response to hypoxia  negative regulation of skeletal muscle cell differentiation  
Ontology : EGO-EBIruffle  calcium ion binding  protein binding  extracellular region  extracellular space  nucleus  cytoplasm  cytoplasm  axonogenesis  central nervous system development  learning or memory  memory  zinc ion binding  cell proliferation  positive regulation of cell proliferation  regulation of cell shape  identical protein binding  protein homodimerization activity  protein homodimerization activity  neuronal cell body  positive regulation of apoptotic process  positive regulation of I-kappaB kinase/NF-kappaB signaling  S100 protein binding  innate immune response  tau protein binding  regulation of neuronal synaptic plasticity  calcium-dependent protein binding  perinuclear region of cytoplasm  astrocyte differentiation  RAGE receptor binding  response to glucocorticoid  response to methylmercury  long-term synaptic potentiation  cellular response to hypoxia  negative regulation of skeletal muscle cell differentiation  
REACTOMEP04271 [protein]
REACTOME PathwaysR-HSA-933542 [pathway]   
NDEx NetworkS100B
Atlas of Cancer Signalling NetworkS100B
Wikipedia pathwaysS100B
Orthology - Evolution
OrthoDB6285
GeneTree (enSembl)ENSG00000160307
Phylogenetic Trees/Animal Genes : TreeFamS100B
HOVERGENP04271
HOGENOMP04271
Homologs : HomoloGeneS100B
Homology/Alignments : Family Browser (UCSC)S100B
Gene fusions - Rearrangements
Fusion : MitelmanS100B/TCTN1 [21q22.3/12q24.11]  
Fusion: TCGA_MDACCS100B 21q22.3 TCTN1 12q24.11 SKCM
Tumor Fusion PortalS100B
Fusion Cancer (Beijing)JUND [19p13.11]  -  S100B [21q22.3]  [FUSC003836]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerS100B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)S100B
dbVarS100B
ClinVarS100B
1000_GenomesS100B 
Exome Variant ServerS100B
ExAC (Exome Aggregation Consortium)ENSG00000160307
GNOMAD BrowserENSG00000160307
Genetic variants : HAPMAP6285
Genomic Variants (DGV)S100B [DGVbeta]
DECIPHERS100B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisS100B 
Mutations
ICGC Data PortalS100B 
TCGA Data PortalS100B 
Broad Tumor PortalS100B
OASIS PortalS100B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICS100B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDS100B
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch S100B
DgiDB (Drug Gene Interaction Database)S100B
DoCM (Curated mutations)S100B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)S100B (select a term)
intoGenS100B
NCG5 (London)S100B
Cancer3DS100B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM176990   
Orphanet
DisGeNETS100B
MedgenS100B
Genetic Testing Registry S100B
NextProtP04271 [Medical]
TSGene6285
GENETestsS100B
Target ValidationS100B
Huge Navigator S100B [HugePedia]
snp3D : Map Gene to Disease6285
BioCentury BCIQS100B
ClinGenS100B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6285
Chemical/Pharm GKB GenePA34912
Clinical trialS100B
Miscellaneous
canSAR (ICR)S100B (select the gene name)
Probes
Litterature
PubMed336 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineS100B
EVEXS100B
GoPubMedS100B
iHOPS100B
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 15:02:14 CET 2017

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