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    ELOB elongin B [ Homo sapiens (human) ]

    Gene ID: 6923, updated on 7-Apr-2024

    Summary

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    Official Symbol
    ELOBprovided by HGNC
    Official Full Name
    elongin Bprovided by HGNC
    Primary source
    HGNC:HGNC:11619
    See related
    Ensembl:ENSG00000103363 MIM:600787; AllianceGenome:HGNC:11619
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SIII; TCEB2
    Summary
    This gene encodes the protein elongin B, which is a subunit of the transcription factor B (SIII) complex. The SIII complex is composed of elongins A/A2, B and C. It activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin A functions as the transcriptionally active component of the SIII complex, whereas elongins B and C are regulatory subunits. Elongin A2 is specifically expressed in the testis, and capable of forming a stable complex with elongins B and C. The von Hippel-Lindau tumor suppressor protein binds to elongins B and C, and thereby inhibits transcription elongation. Two alternatively spliced transcript variants encoding different isoforms have been described for this gene. Pseudogenes have been identified on chromosomes 11 and 13. [provided by RefSeq, Aug 2008]
    Expression
    Ubiquitous expression in testis (RPKM 67.4), adrenal (RPKM 41.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ELOB in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (2771414..2777280, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2791632..2797493, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2821415..2827281, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2788581-2789158 Neighboring gene SRRM2 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:2801519-2802361 and GRCh37_chr16:2802362-2803204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2803205-2804047 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:2807529-2808728 Neighboring gene serine/arginine repetitive matrix 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2819013-2819715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2819716-2820419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2820420-2821122 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:2823070-2823222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2828259-2829193 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2829194-2830127 Neighboring gene serine protease 33 Neighboring gene small nucleolar RNA, H/ACA box 3C

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. TCEB2 confers resistance to VEGF-targeted therapy in ovarian cancer. Deng Z, et al. Oncol Rep, 2016 Jan. PMID 26531153
    2. Elongin B-mediated epigenetic alteration of viral chromatin correlates with efficient human cytomegalovirus gene expression and replication. Hwang J, et al. mBio, 2011. PMID 21447700, Free PMC Article
    3. Structural insights into the dual-targeting mechanism of Nutlin-3. Shin JS, et al. Biochem Biophys Res Commun, 2012 Mar 30. PMID 22402281
    4. Movement pattern recognition in basketball free-throw shooting. Schmidt A. Hum Mov Sci, 2012 Apr. PMID 22402277
    5. Positive regulation of general transcription factor SIII by a tailed ubiquitin homolog. Garrett KP, et al. Proc Natl Acad Sci U S A, 1995 Aug 1. PMID 7638163, Free PMC Article

    See all (282) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study shows that TCEB2 is involved in the development of acquired resistance to bevacizumab in ovarian cancer cells via the mechanisms of suppression of VEGF-A expression by promoting HIF-1alpha degradation and induction of interleukin-8 (IL-8) expression.
      Title: TCEB2 confers resistance to VEGF-targeted therapy in ovarian cancer.
    2. crystals of SOCS2 in complex with its adaptor proteins, Elongin C and Elongin B, underwent a change in crystallographic parameters when treated with dimethyl sulfoxide during soaking experiments.
      Title: Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases.
    3. The crystal structure of VHL bound to a Cul2 N-terminal domain, Elongin B, and Elongin C.
      Title: Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex.
    4. Vif interaction with EloB-EloC may contribute to recruitment of CBF-beta to Vif, demonstrating that the EloB C-teminus may play a role in improving Vif function and that the over-expression of EloB results in Vif stabilization.
      Title: Interactions between HIV-1 Vif and human ElonginB-ElonginC are important for CBF-β binding to Vif.
    5. ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain.
      Title: Multimeric complexes among ankyrin-repeat and SOCS-box protein 9 (ASB9), ElonginBC, and Cullin 5: insights into the structure and assembly of ECS-type Cullin-RING E3 ubiquitin ligases.
    6. Elongin B also enhances gene expression from the double-stranded DNA genome of human cytomegalovirus.
      Title: Elongin B-mediated epigenetic alteration of viral chromatin correlates with efficient human cytomegalovirus gene expression and replication.
    7. Recombinant full-length Vif interacted with the Elongin BC complex in vitro with a K(d) of 1.9 muM and resulted in observable changes in deuterium uptake in both Elongin C and B.
      Title: Molecular insight into the conformational dynamics of the Elongin BC complex and its interaction with HIV-1 Vif.
    8. Elongin B/C recruitment regulates substrate binding by CIS
      Title: Elongin B/C recruitment regulates substrate binding by CIS.
    9. nuclear level of active P-TEFb is controlled by dynamic and reversible remodelling of 7SK snRNP
      Title: Dynamic remodelling of human 7SK snRNP controls the nuclear level of active P-TEFb.
    10. the E3 ubiquitin ligase activity of the Vif-BC-Cul5 complex is essential for Vif function against APOBEC3G
      Title: Ubiquitination of APOBEC3G by an HIV-1 Vif-Cullin5-Elongin B-Elongin C complex is essential for Vif function.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat The C-terminal 34 residues (1329-1362) of BRD4 are crucial for interaction with P-TEFb. Overexpression of the BRD4 P-TEFb-interacting domain disrupts the interaction between HIV-1 Tat and P-TEFb PubMed
    tat HIV-1 Tat directly interacts with elongin B as demonstrated by Tat-affinity column purification PubMed
    Vif vif HIV-1 complexes with TCEB2 (ELOB) PubMed
    vif ASK1 inhibits the interaction of HIV-1 Vif with ELOB/C in a dose-dependent manner, whereas no significant change is observed in the binding of Vif with CUL5 or CBFbeta PubMed
    vif CUL5/RBX2/ELOB/ELOC/Vif/CBF-beta complex catalyzes polyubiquitin chain formation on A3G in the presence of ubiquitin E2 UBE2R1 (CDC34) or UBCH5b (UBE2D2) PubMed
    vif HIV-1 Vif, CBF-beta, CUL5, and ELOB/C form a complex that is required for Vif-mediated downregulation of A3G and A3F. CBF-beta regulates HIV-1 infectivity only in the presence of A3G PubMed
    vif An overall crystal structure indicates that the Vif-CBF-beta-CUL5-ELOB-ELOC complex has a U-shape architecture, including the two straight arms Vif-CBF-beta and CUL5 and the bent arm formation between ELOC and CUL5 and Vif interactions PubMed
    vif HIV-1 Vif (amino acids 144-149; SLQXLA motif) interacts with cellular proteins Cul5, elongins B and C, and Rbx1 to form an Skp1-Cullin-F-box (SCF)-like complex that allows Vif to interact with APOBEC3G and induce its ubiquitination and degradation PubMed
    vif HIV-1 Vif mutants W5S, W21S, W38S, W89S, F112S, and F115S have a reduced ability to interact with CBF-beta, but these Vif hydrophobic residue mutations still interact with EloB PubMed
    vif Simultaneous substitution of the three Vif-interacting residues L52, W53, and D55 and the two ELOC-interacting residues P41 and H48 in CUL5 impairs the ability of CUL5 to interact with the Vif-CBF-beta-ELOB-ELOC protein complex PubMed
    vif The absence of Vif-CBF-beta reduces the interaction between the CUL5 and the EloC-EloB complex, indicating that the former two proteins have a critical role in promoting assembly of the pentameric complex PubMed
    vif The PPLP motif (residues 161-164) of HIV-1 Vif binds to the C-terminal region (residues 101-118) of ElonginB PubMed
    vif Overexpression of EloB increases HIV-1 Vif stability in cells. The N-terminal residues 9-14 of EloB are involved in EloB-mediated stability of Vif PubMed
    vif The interaction of HIV-1 Vif with EloB/EloC complex is important for the binding of Vif to CBF-beta in cells. The Vif SOCS box mutant (SLQ to AAA) significantly disrupt its interaction with the EloB/EloC complex PubMed
    vif The interaction between the HIV-1 Vif PPLP motif (residues 161-164) and the 34-amino-acid C-terminal tail (residues 85-118) of EloB plays a role in promoting recruitment of CBF-beta to the Vif-Cul5 E3 complex PubMed
    vif The solubility of HIV-1 Vif is significantly enhanced by co-expression of EloB, EloC, and CBF-beta in vitro PubMed
    vif The substitution of Leu64 or Ile66 with serine abolishes the ability of CBF-beta to interact with the Vif-EloB/EloC complex, while the substitution of Thr68 or Tyr69 with alanine has an intermediate effect on the interaction of CBF-beta with the complex PubMed
    vif Amino acid residues Vif135-158 have the most binding to the Elongin BC complex and undergo a structural change in the presence of Elongin BC PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of proteasomal ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein-containing complex assembly TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in target-directed miRNA degradation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription elongation by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription initiation at RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul2-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Cul5-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of VCB complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of elongin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of elongin complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    elongin-B
    Names
    RNA polymerase II transcription factor SIII p18 subunit
    RNA polymerase II transcription factor SIII subunit B
    SIII p18
    elongin 18 kDa subunit
    elongin, 18-kD subunit
    epididymis secretory sperm binding protein
    transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)
    transcription elongation factor B polypeptide 2
    transcription elongation factor B subunit 2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_007108.4 → NP_009039.1  elongin-B isoform a

      See identical proteins and their annotated locations for NP_009039.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (a).
      Source sequence(s)
      AC092117, BC013306, DT217333
      Consensus CDS
      CCDS45387.1
      UniProtKB/Swiss-Prot
      B7WPD3, Q15370
      UniProtKB/TrEMBL
      B8ZZU8, D3DU99
      Related
      ENSP00000386652.5, ENST00000409906.9
      Conserved Domains (1) summary
      cd01788
      Location:2 → 102
      Ubl_ElonginB; ubiquitin-like (Ubl) domain found in transcription elongation factor B (Elongin B) and similar proteins

    2. NM_207013.3 → NP_996896.1  elongin-B isoform b

      See identical proteins and their annotated locations for NP_996896.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment in the 3' region, resulting in a downstream stop codon, compared to variant 1. The resulting isoform (b) has a longer C-terminus, compared to isoform a.
      Source sequence(s)
      AC092117, BC013306, BM700019
      Consensus CDS
      CCDS32374.1
      UniProtKB/TrEMBL
      A0A384MDL3
      Related
      ENSP00000262306.7, ENST00000262306.11
      Conserved Domains (1) summary
      cd01788
      Location:1 → 118
      ElonginB; Ubiquitin-like domain of Elongin B

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      2771414..2777280 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      2791632..2797493 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_001582.3: Suppressed sequence

      Description
      NG_001582.3: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15370.1 GenPept UniProtKB/Swiss-Prot:Q15370

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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