Human Gene PSMB4 (uc001eyc.1)
  Description: Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4), mRNA.
RefSeq Summary (NM_002796): The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:151,372,041-151,374,412 Size: 2,372 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr1:151,372,064-151,374,305 Size: 2,242 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:151,372,041-151,374,412)mRNA (may differ from genome)Protein (264 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PSB4_HUMAN
DESCRIPTION: RecName: Full=Proteasome subunit beta type-4; Short=Proteasome beta chain; EC=3.4.25.1; AltName: Full=26 kDa prosomal protein; Short=HsBPROS26; Short=PROS-26; AltName: Full=Macropain beta chain; AltName: Full=Multicatalytic endopeptidase complex beta chain; AltName: Full=Proteasome chain 3; Short=HsN3; Flags: Precursor;
FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. Mediates the lipopolysaccharide-induced signal macrophage proteasome (By similarity). SMAD1/OAZ1/PSMB4 complex mediates the degradation of the CREBBP/EP300 repressor SNIP1.
CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.
SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with HIV-1 TAT and HIV-1 NEF proteins. Interaction with HTLV-1 TAX protein favors NFKB1 activation. Interacts with bacterial lipopolysaccharide (LPS) (By similarity). Forms a ternary complex with SMAD1 and OAZ1 before PSMB4 is incorporated into the 20S proteasome. Interacts with PRPF19.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).
INDUCTION: Up-regulated in fibrolamellar carcinomas.
SIMILARITY: Belongs to the peptidase T1B family.

-  Primer design for this transcript
 

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-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PSMB4
CDC HuGE Published Literature: PSMB4

-  MalaCards Disease Associations
  MalaCards Gene Search: PSMB4
Diseases sorted by gene-association score: fallopian tube carcinoma (7), cystic fibrosis (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 210.11 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 6530.83 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00230.000 Picture PostScript Text
3' UTR -16.00107-0.150 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
IPR016050 - Proteasome_bsu_CS
IPR016295 - Proteasome_endopept_cplx_B
IPR001353 - Proteasome_sua/b
IPR023333 - Proteasome_suB-type

Pfam Domains:
PF00227 - Proteasome subunit

SCOP Domains:
56235 - N-terminal nucleophile aminohydrolases (Ntn hydrolases)

ModBase Predicted Comparative 3D Structure on P28070
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-  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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
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 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001530 lipopolysaccharide binding
GO:0004175 endopeptidase activity
GO:0004298 threonine-type endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0002862 negative regulation of inflammatory response to antigenic stimulus
GO:0006508 proteolysis
GO:0016032 viral process
GO:0016579 protein deubiquitination
GO:0043687 post-translational protein modification
GO:0051603 proteolysis involved in cellular protein catabolic process

Cellular Component:
GO:0000502 proteasome complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005839 proteasome core complex
GO:0019774 proteasome core complex, beta-subunit complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF206225 - JP 2014500723-A/13728: Polycomb-Associated Non-Coding RNAs.
AK313825 - Homo sapiens cDNA, FLJ94446, highly similar to Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4), mRNA.
AK294149 - Homo sapiens cDNA FLJ56661 complete cds, highly similar to Proteasome subunit beta type 4 precursor (EC 3.4.25.1).
D26600 - Homo sapiens mRNA for proteasome subunit HsN3, complete cds.
HM005586 - Homo sapiens clone HTL-S-46 testis tissue sperm-binding protein Li 79P mRNA, complete cds.
BC008314 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:3143023).
BC010088 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:2967687).
BC010098 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:3505166).
BC011768 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:3607881).
BC012168 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:4640238).
BC017451 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:3543917).
BC017486 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:3536964).
BC000331 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4, mRNA (cDNA clone IMAGE:2822513).
AB464086 - Synthetic construct DNA, clone: pF1KB5566, Homo sapiens PSMB4 gene for proteasome (prosome, macropain) subunit, beta type 4, without stop codon, in Flexi system.
CR456820 - Homo sapiens full open reading frame cDNA clone RZPDo834E0215D for gene PSMB4, proteasome (prosome, macropain) subunit, beta type, 4; complete cds, incl. stopcodon.
CU675936 - Synthetic construct Homo sapiens gateway clone IMAGE:100016923 5' read PSMB4 mRNA.
CU679615 - Synthetic construct Homo sapiens gateway clone IMAGE:100016925 5' read PSMB4 mRNA.
CU680252 - Synthetic construct Homo sapiens gateway clone IMAGE:100016928 5' read PSMB4 mRNA.
CU678915 - Synthetic construct Homo sapiens gateway clone IMAGE:100016924 5' read PSMB4 mRNA.
BT006917 - Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4 mRNA, complete cds.
DQ890748 - Synthetic construct clone IMAGE:100003378; FLH165650.01X; RZPDo839E12160D proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4) gene, encodes complete protein.
DQ892020 - Synthetic construct clone IMAGE:100004650; FLH182399.01X; RZPDo839F10138D proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4) gene, encodes complete protein.
DQ895212 - Synthetic construct Homo sapiens clone IMAGE:100009672; FLH182395.01L; RZPDo839F10137D proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4) gene, encodes complete protein.
KJ905874 - Synthetic construct Homo sapiens clone ccsbBroadEn_15544 PSMB4 gene, encodes complete protein.
KJ905875 - Synthetic construct Homo sapiens clone ccsbBroadEn_15545 PSMB4 gene, encodes complete protein.
KJ905876 - Synthetic construct Homo sapiens clone ccsbBroadEn_15546 PSMB4 gene, encodes complete protein.
KJ897405 - Synthetic construct Homo sapiens clone ccsbBroadEn_06799 PSMB4 gene, encodes complete protein.
S71381 - prosome beta-subunit=multicatalytic proteinase complex [human, lymphoma, mRNA, 959 nt].
LF352467 - JP 2014500723-A/159970: Polycomb-Associated Non-Coding RNAs.
JD557794 - Sequence 538818 from Patent EP1572962.
MA588044 - JP 2018138019-A/159970: Polycomb-Associated Non-Coding RNAs.
MA441802 - JP 2018138019-A/13728: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03050 - Proteasome

BioCyc Knowledge Library
PWY3DJ-213 - Targeted protein degradation

Reactome (by CSHL, EBI, and GO)

Protein P28070 (Reactome details) participates in the following event(s):

R-HSA-5665871 ADRM1 binds 26S proteasome
R-HSA-8956140 NEDD8 and UBD bind NUB1 and the 26S proteasome
R-HSA-5665854 ADRM1:26S proteaseome binds UCHL5
R-HSA-5689539 ADRM1:26S proteaseome binds USP14
R-HSA-5689603 UCH proteinases
R-HSA-8951664 Neddylation
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-68827 CDT1 association with the CDC6:ORC:origin complex
R-HSA-68949 Orc1 removal from chromatin
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6
R-HSA-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-HSA-69229 Ubiquitin-dependent degradation of Cyclin D1
R-HSA-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
R-HSA-174154 APC/C:Cdc20 mediated degradation of Securin
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1
R-HSA-174184 Cdc20:Phospho-APC/C mediated degradation of Cyclin A
R-HSA-180534 Vpu mediated degradation of CD4
R-HSA-180585 Vif-mediated degradation of APOBEC3G
R-HSA-9020702 Interleukin-1 signaling
R-HSA-211733 Regulation of activated PAK-2p34 by proteasome mediated degradation
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-HSA-350562 Regulation of ornithine decarboxylase (ODC)
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1169091 Activation of NF-kappaB in B cells
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-1236974 ER-Phagosome pathway
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes)
R-HSA-4641258 Degradation of DVL
R-HSA-195253 Degradation of beta-catenin by the destruction complex
R-HSA-4641257 Degradation of AXIN
R-HSA-4608870 Asymmetric localization of PCP proteins
R-HSA-5358346 Hedgehog ligand biogenesis
R-HSA-5362768 Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
R-HSA-202424 Downstream TCR signaling
R-HSA-2871837 FCERI mediated NF-kB activation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-HSA-5676590 NIK-->noncanonical NF-kB signaling
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome
R-HSA-5610783 Degradation of GLI2 by the proteasome
R-HSA-5610780 Degradation of GLI1 by the proteasome
R-HSA-5632684 Hedgehog 'on' state
R-HSA-5658442 Regulation of RAS by GAPs
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-5687128 MAPK6/MAPK4 signaling
R-HSA-8948751 Regulation of PTEN stability and activity
R-HSA-69481 G2/M Checkpoints
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-5678895 Defective CFTR causes cystic fibrosis
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-8939902 Regulation of RUNX2 expression and activity
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C
R-HSA-187577 SCF(Skp2)-mediated degradation of p27/p21
R-HSA-8941858 Regulation of RUNX3 expression and activity
R-HSA-392499 Metabolism of proteins
R-HSA-68867 Assembly of the pre-replicative complex
R-HSA-69052 Switching of origins to a post-replicative state
R-HSA-69610 p53-Independent DNA Damage Response
R-HSA-75815 Ubiquitin-dependent degradation of Cyclin D
R-HSA-174143 APC/C-mediated degradation of cell cycle proteins
R-HSA-176409 APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-68882 Mitotic Anaphase
R-HSA-176408 Regulation of APC/C activators between G1/S and early anaphase
R-HSA-179419 APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint
R-HSA-162909 Host Interactions of HIV factors
R-HSA-446652 Interleukin-1 family signaling
R-HSA-169911 Regulation of Apoptosis
R-HSA-69541 Stabilization of p53
R-HSA-351202 Metabolism of polyamines
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR)
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-4086400 PCP/CE pathway
R-HSA-5358351 Signaling by Hedgehog
R-HSA-5387390 Hh mutants abrogate ligand secretion
R-HSA-202403 TCR signaling
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-5610787 Hedgehog 'off' state
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-5683057 MAPK family signaling cascades
R-HSA-6807070 PTEN Regulation
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-69275 G2/M Transition
R-HSA-382551 Transport of small molecules
R-HSA-5619084 ABC transporter disorders
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-8878166 Transcriptional regulation by RUNX2
R-HSA-376176 Signaling by ROBO receptors
R-HSA-69202 Cyclin E associated events during G1/S transition
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-69002 DNA Replication Pre-Initiation
R-HSA-69239 Synthesis of DNA
R-HSA-69613 p53-Independent G1/S DNA damage checkpoint
R-HSA-69242 S Phase
R-HSA-453276 Regulation of mitotic cell cycle
R-HSA-176814 Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-162906 HIV Infection
R-HSA-449147 Signaling by Interleukins
R-HSA-109581 Apoptosis
R-HSA-69563 p53-Dependent G1 DNA Damage Response
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-8953854 Metabolism of RNA
R-HSA-1280218 Adaptive Immune System
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-2262749 Cellular response to hypoxia
R-HSA-162582 Signal Transduction
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-168249 Innate Immune System
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-168256 Immune System
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-1640170 Cell Cycle
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-5619115 Disorders of transmembrane transporters
R-HSA-212436 Generic Transcription Pathway
R-HSA-422475 Axon guidance
R-HSA-69206 G1/S Transition
R-HSA-68874 M/G1 Transition
R-HSA-69306 DNA Replication
R-HSA-69615 G1/S DNA Damage Checkpoints
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-68886 M Phase
R-HSA-5663205 Infectious disease
R-HSA-5357801 Programmed Cell Death
R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint
R-HSA-1430728 Metabolism
R-HSA-2262752 Cellular responses to stress
R-HSA-1643685 Disease
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-1266738 Developmental Biology
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9L3, NM_002796, NP_002787, P28070, P31148, PROS26, PSB4_HUMAN, Q5SZS5, Q6IBI4, Q969L6
UCSC ID: uc001eyc.1
RefSeq Accession: NM_002796
Protein: P28070 (aka PSB4_HUMAN)
CCDS: CCDS996.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002796.2
exon count: 7CDS single in 3' UTR: no RNA size: 925
ORF size: 795CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1790.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.