ELOB elongin B [Homo sapiens (human)] - Gene

Summary

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

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
Elongin B/C recruitment regulates substrate binding by CIS
Title: Elongin B/C recruitment regulates substrate binding by CIS.
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.
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)

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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-61169 (e-PCR)
- UniSTS:69899

D16S2844 (e-PCR)
- UniSTS:153414

D16S2549E (e-PCR)
- UniSTS:151638

RH122227 (e-PCR)
- UniSTS:134776

D9S2087 (e-PCR)
- UniSTS:35199

RH92618 (e-PCR)
- UniSTS:85420

SHGC-61065 (e-PCR)
- UniSTS:15792

SHGC-32846 (e-PCR)
- UniSTS:11735

RH44069 (e-PCR)
- UniSTS:50649

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)

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
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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

2771414..2777280 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

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.