Human Gene SH3KBP1 (ENST00000397821.8_8) from GENCODE V47lift37
  Description: SH3 domain containing kinase binding protein 1, transcript variant 1 (from RefSeq NM_031892.3)
Gencode Transcript: ENST00000397821.8_8
Gencode Gene: ENSG00000147010.19_12
Transcript (Including UTRs)
   Position: hg19 chrX:19,552,095-19,905,718 Size: 353,624 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chrX:19,554,535-19,905,428 Size: 350,894 Coding Exon Count: 18 

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Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:19,552,095-19,905,718)mRNA (may differ from genome)Protein (665 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SH3K1_HUMAN
DESCRIPTION: RecName: Full=SH3 domain-containing kinase-binding protein 1; AltName: Full=CD2-binding protein 3; Short=CD2BP3; AltName: Full=Cbl-interacting protein of 85 kDa; AltName: Full=Human Src family kinase-binding protein 1; Short=HSB-1;
FUNCTION: Adapter protein involved in regulating diverse signal transduction pathways. Involved in the regulation of endocytosis and lysosomal degradation of ligand-induced receptor tyrosine kinases, including EGFR and MET/hepatocyte growth factor receptor, through a association with CBL and endophilins. The association with CBL, and thus the receptor internalization, may inhibited by an interaction with PDCD6IP and/or SPRY2. Involved in regulation of ligand-dependent endocytosis of the IgE receptor. Attenuates phosphatidylinositol 3-kinase activity by interaction with its regulatory subunit (By similarity). May be involved in regulation of cell adhesion; promotes the interaction between TTK2B and PDCD6IP. May be involved in the regulation of cellular stress response via the MAPK pathways through its interaction with MAP3K4. Is involved in modulation of tumor necrosis factor mediated apoptosis. Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration.
SUBUNIT: Can self-associate and form homotetramers. Interacts with CD2, F-actin capping protein, PIK3R3, GRB2, EGFR, MET, BLNK, MAP3K4, PDCD6IP, SPRY2, ARHGAP17, ARHGAP27, MAGI2, CRK, BCAR1, SOS1, ASAP1, ARAP3, HIP1R, SYNJ2, INPP5D and STAP1. Interacts with CBL and CBLB, but does not interact with CBLC. Two molecules of SH3KBP1 seem to bind through their respective SH3 1 domain to one molecule of CBLB. The interaction with CBL or CBLB and EGFR is increased upon EGF stimulation. The interaction with CBL is attenuated by PDCD6IP. Interacts through its proline-rich region with the SH3 domain of endophilins SH3GL1, SH3GL2 and SH3GL3. The SH3KBP1-endophilin complex seems to associate with a complex containing the phosphorylated receptor (EGFR or MET) and phosphorylated CBL. Probably associates with ASAP1 and phosphorylated EGFR. Probably part of a complex consisting of at least SH3KBP1, ASAP1 and ARAP3. Interacts with focal adhesion kinases PTK2/FAK1 AND PTK2B/PYK2, probably as a dimer. Interacts with DAB2 and probably associates with chathrin through its interaction with DAB2. Part of a complex consisting of SH3KBP1, DAB2, and clathrin heavy chain. DAB2 and clathrin dissociate from SH3KBP1 following growth factor treatment, enabling interaction with CBL. Interacts with DDN and probably associates with MAGI2 through its interaction with DDN. Interacts with the SH3 domains of SRC tyrosine-protein kinases SRC, LCK, LYN, FGR, FYN and HCK. Interacts with TRADD, BIRC2, TRAF1, TRAF2 and TNFR1, and the association with a TNFR1-associated complex upon stimulation with TNF-alpha seems to be mediated by SRC. Probably interacts with SH3KBP1.
INTERACTION: P22681:CBL; NbExp=2; IntAct=EBI-346595, EBI-518228; P98078:Dab2 (xeno); NbExp=9; IntAct=EBI-346595, EBI-1391846; O94850:DDN; NbExp=5; IntAct=EBI-346595, EBI-5240523;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Cytoplasmic vesicle membrane; Peripheral membrane protein. Cell junction, synapse, synaptosome. Cell junction, focal adhesion (By similarity). Note=Localized in endocytic vesicles containing clustered receptors. Colocalizes with ASAP1 in vesicular structures. Colocalized with actin microfilaments and focal adhesions (By similarity). Colocalized with MAGI2 in synaptosomes (By similarity).
TISSUE SPECIFICITY: Ubiquitously expressed. Also expressed in some cancer cell lines.
DOMAIN: The SH3 domains mediate interaction with SHKBP1 (By similarity).
PTM: Monoubiquitinated by CBL and CBLB after EGF stimulation; probably on its C-terminus.
SIMILARITY: Contains 3 SH3 domains.
SEQUENCE CAUTION: Sequence=AAH50663.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SH3KBP1
Diseases sorted by gene-association score: adrenal cortical adenocarcinoma (2), breast adenocarcinoma (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 61.71 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 429.79 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -134.10290-0.462 Picture PostScript Text
3' UTR -634.102440-0.260 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000108 - p67phox
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
82061 - BAH domain
50044 - SH3-domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2BZ8 - X-ray MuPIT 2K6D - NMR MuPIT 2K9G - NMR MuPIT 2O2O - NMR MuPIT 2YDL - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96B97
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017124 SH3 domain binding

Biological Process:
GO:0006897 endocytosis
GO:0006915 apoptotic process
GO:0007010 cytoskeleton organization
GO:0007267 cell-cell signaling
GO:0007411 axon guidance
GO:0008360 regulation of cell shape
GO:0016477 cell migration
GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway
GO:0061024 membrane organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030054 cell junction
GO:0030139 endocytic vesicle
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0043005 neuron projection
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AF230904 - Homo sapiens c-Cbl-interacting protein (CIN85) mRNA, complete cds.
AY423734 - Homo sapiens migration-inducing gene 18 protein mRNA, complete cds.
AF542051 - Homo sapiens CD2 binding protein CD2BP3 mRNA, complete cds; alternatively spliced.
BC015806 - Homo sapiens SH3-domain kinase binding protein 1, mRNA (cDNA clone MGC:9446 IMAGE:3906722), complete cds.
AK293234 - Homo sapiens cDNA FLJ54623 complete cds, highly similar to SH3-domain kinase-binding protein 1.
AK300189 - Homo sapiens cDNA FLJ59425 complete cds, highly similar to SH3-domain kinase-binding protein 1.
AK293237 - Homo sapiens cDNA FLJ54612 complete cds, highly similar to SH3-domain kinase-binding protein 1.
AY542305 - Homo sapiens GIG10 mRNA, complete cds.
AF329267 - Homo sapiens SH3-domain kinase binding protein 1 (SH3KBP1) mRNA, complete cds.
AF329268 - Homo sapiens SH3-domain kinase binding protein 1 (SH3KBP1) mRNA, complete cds.
AK313308 - Homo sapiens cDNA, FLJ93821, Homo sapiens SH3-domain kinase binding protein 1 (SH3KBP1), mRNA.
KJ898766 - Synthetic construct Homo sapiens clone ccsbBroadEn_08160 SH3KBP1 gene, encodes complete protein.
DQ892387 - Synthetic construct clone IMAGE:100005017; FLH185847.01X; RZPDo839F09148D SH3-domain kinase binding protein 1 (SH3KBP1) gene, encodes complete protein.
DQ895600 - Synthetic construct Homo sapiens clone IMAGE:100010060; FLH185843.01L; RZPDo839F09147D SH3-domain kinase binding protein 1 (SH3KBP1) gene, encodes complete protein.
AB590253 - Synthetic construct DNA, clone: pFN21AE1466, Homo sapiens SH3KBP1 gene for SH3-domain kinase binding protein 1, without stop codon, in Flexi system.
CU677457 - Synthetic construct Homo sapiens gateway clone IMAGE:100019992 5' read SH3KBP1 mRNA.
BC050663 - Homo sapiens SH3-domain kinase binding protein 1, mRNA (cDNA clone IMAGE:4421051), partial cds.
BC041055 - Homo sapiens cDNA clone IMAGE:5432927, partial cds.
JD347814 - Sequence 328838 from Patent EP1572962.
JD127253 - Sequence 108277 from Patent EP1572962.
JD356732 - Sequence 337756 from Patent EP1572962.
JD288048 - Sequence 269072 from Patent EP1572962.
JD512947 - Sequence 493971 from Patent EP1572962.
JD501609 - Sequence 482633 from Patent EP1572962.
DL492492 - Novel nucleic acids.
DL490962 - Novel nucleic acids.
JD067438 - Sequence 48462 from Patent EP1572962.
JD300340 - Sequence 281364 from Patent EP1572962.
AK307276 - Homo sapiens cDNA, FLJ97224.
JD458927 - Sequence 439951 from Patent EP1572962.
JD370399 - Sequence 351423 from Patent EP1572962.
JD142035 - Sequence 123059 from Patent EP1572962.
JD068600 - Sequence 49624 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_cblPathway - CBL mediated ligand-induced downregulation of EGF receptors

Reactome (by CSHL, EBI, and GO)

Protein Q96B97 (Reactome details) participates in the following event(s):

R-HSA-8855259 RELN:VLDLR:DAB1 binds SH3KBP1
R-HSA-983703 p-6Y-SYK phosphorylates BLNK (SLP65)
R-HSA-8855237 FYN phosphorylates DAB1 in RELN:VLDLR:DAB1:SH3KBP1
R-HSA-182994 Assembly of EGFR complex in clathrin-coated vesicles
R-HSA-183072 EGFR non-clathrin mediated endocytosis
R-HSA-8875482 CBL recruits CIN85:endophilin to ubiquitinated MET
R-HSA-8876255 CBL recruits CIN85:endophilin complex to InlB-bound MET
R-HSA-8951490 CIN85 dissociates from EGF:p-6Y-EGFR:CBL:Beta-Pix:CDC42:GTP:CIN85
R-HSA-182986 CBL-mediated ubiquitination of CIN85
R-HSA-183002 Beta-Pix:CDC42:GTP binds CBL in EGF:p-6Y-EGFR:CBL:CIN85
R-HSA-8867044 EGFR binds EPS15, EPN1, EPS15L1
R-HSA-182990 Sprouty sequesters CBL away from active EGFR
R-HSA-8876262 EPS15 and HGS bind CBL-monoubiquitinated MET engaged with Listeria InlB
R-HSA-1112666 BLNK (SLP-65) Signalosome hydrolyzes phosphatidyinositol bisphosphate forming diacylglycerol and inositol-1,4,5-trisphosphate
R-HSA-8867041 EGFR phosphorylates EPS15
R-HSA-8867047 PTPN3 dephosphorylates EPS15
R-HSA-8866279 Epsin family proteins bind ubiquitinated cargo
R-HSA-8875490 EPS15 and HGS bind ubiquitinated MET
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8866376 Reelin signalling pathway
R-HSA-983695 Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
R-HSA-422475 Axon guidance
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-182971 EGFR downregulation
R-HSA-6807004 Negative regulation of MET activity
R-HSA-8875360 InlB-mediated entry of Listeria monocytogenes into host cell
R-HSA-1266738 Developmental Biology
R-HSA-1280218 Adaptive Immune System
R-HSA-177929 Signaling by EGFR
R-HSA-6806834 Signaling by MET
R-HSA-8876384 Listeria monocytogenes entry into host cells
R-HSA-168256 Immune System
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-5663205 Infectious disease
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-162582 Signal Transduction
R-HSA-1643685 Disease
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z1D5, CIN85, ENST00000397821.1, ENST00000397821.2, ENST00000397821.3, ENST00000397821.4, ENST00000397821.5, ENST00000397821.6, ENST00000397821.7, NM_031892, Q5JPT4, Q5JPT5, Q8IWX6, Q8IX98, Q96B97, Q96RN4, Q9NYR0, SH3K1_HUMAN, uc318zhu.1, uc318zhu.2
UCSC ID: ENST00000397821.8_8
RefSeq Accession: NM_031892.3
Protein: Q96B97 (aka SH3K1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.