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Protein

COP9 signalosome complex subunit 4

Gene

COPS4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. Also involved in the deneddylation of non-cullin subunits such as STON2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1, IRF8/ICSBP and SNAPIN, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.6 Publications

GO - Biological processi

  • cullin deneddylation Source: UniProtKB
  • nucleotide-excision repair, DNA damage recognition Source: Reactome
  • protein deneddylation Source: UniProtKB
  • transcription-coupled nucleotide-excision repair Source: Reactome
Complete GO annotation...

Enzyme and pathway databases

BioCyciZFISH:ENSG00000138663-MONOMER.
ReactomeiR-HSA-5696394. DNA Damage Recognition in GG-NER.
R-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-8856825. Cargo recognition for clathrin-mediated endocytosis.

Names & Taxonomyi

Protein namesi
Recommended name:
COP9 signalosome complex subunit 4
Short name:
SGN4
Short name:
Signalosome subunit 4
Alternative name(s):
JAB1-containing signalosome subunit 4
Gene namesi
Name:COPS4
Synonyms:CSN4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:16702. COPS4.

Subcellular locationi

GO - Cellular componenti

  • cell junction Source: HPA
  • COP9 signalosome Source: UniProtKB
  • cytosol Source: GO_Central
  • extracellular exosome Source: UniProtKB
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • synaptic vesicle Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cytoplasm, Cytoplasmic vesicle, Nucleus, Signalosome, Synapse

Pathology & Biotechi

Organism-specific databases

DisGeNETi51138.
OpenTargetsiENSG00000138663.
PharmGKBiPA26756.

Polymorphism and mutation databases

BioMutaiCOPS4.
DMDMi55976582.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00001209872 – 406COP9 signalosome complex subunit 4Add BLAST405

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1 Publication1
Modified residuei25N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9BT78.
MaxQBiQ9BT78.
PaxDbiQ9BT78.
PeptideAtlasiQ9BT78.
PRIDEiQ9BT78.

2D gel databases

OGPiQ9BT78.
REPRODUCTION-2DPAGEIPI00171844.

PTM databases

iPTMnetiQ9BT78.
PhosphoSitePlusiQ9BT78.
SwissPalmiQ9BT78.

Expressioni

Gene expression databases

BgeeiENSG00000138663.
CleanExiHS_COPS4.
ExpressionAtlasiQ9BT78. baseline and differential.
GenevisibleiQ9BT78. HS.

Organism-specific databases

HPAiHPA036894.
HPA042828.

Interactioni

Subunit structurei

Component of the CSN complex, composed of COPS1/GPS1, COPS2, COPS3, COPS4, COPS5, COPS6, COPS7 (COPS7A or COPS7B), COPS8 and COPS9 isoform 1 (PubMed:18850735, PubMed:26456823). In the complex, it probably interacts directly with COPS1, COPS2, COPS3, COPS5, COPS6, COPS7 (COPS7A or COPS7B) and COPS8 (PubMed:18850735). Interacts with TOR1A; the interaction is direct and associates TOR1A and SNAPIN with the CSN complex (PubMed:21102408). Interacts with STON2; controls STON2 neddylation levels (PubMed:21102408).3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
C19orf57Q0VDD72EBI-742413,EBI-741210
FOSP011002EBI-742413,EBI-852851
STK11Q158312EBI-742413,EBI-306838
USHBP1Q8N6Y04EBI-742413,EBI-739895

Protein-protein interaction databases

BioGridi119324. 97 interactors.
DIPiDIP-34516N.
IntActiQ9BT78. 29 interactors.
MINTiMINT-1464138.
STRINGi9606.ENSP00000264389.

Structurei

Secondary structure

1406
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 12Combined sources11
Helixi19 – 34Combined sources16
Helixi39 – 53Combined sources15
Helixi59 – 72Combined sources14
Helixi73 – 75Combined sources3
Helixi78 – 92Combined sources15
Helixi93 – 99Combined sources7
Helixi100 – 116Combined sources17
Helixi120 – 128Combined sources9
Turni132 – 134Combined sources3
Beta strandi135 – 137Combined sources3
Helixi141 – 157Combined sources17
Helixi161 – 172Combined sources12
Helixi175 – 177Combined sources3
Helixi181 – 197Combined sources17
Helixi201 – 211Combined sources11
Helixi219 – 235Combined sources17
Helixi240 – 251Combined sources12
Helixi253 – 257Combined sources5
Helixi261 – 268Combined sources8
Helixi275 – 278Combined sources4
Helixi279 – 283Combined sources5
Helixi287 – 290Combined sources4
Helixi299 – 315Combined sources17
Beta strandi317 – 320Combined sources4
Helixi321 – 328Combined sources8
Helixi332 – 344Combined sources13
Beta strandi350 – 353Combined sources4
Turni354 – 357Combined sources4
Beta strandi358 – 361Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4D0PX-ray1.60A1-363[»]
4D10X-ray3.80D/L1-406[»]
4D18X-ray4.08D/L1-406[»]
4WSNX-ray5.50D/L/T/b/j/r1-406[»]
ProteinModelPortaliQ9BT78.
SMRiQ9BT78.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini201 – 363PCIAdd BLAST163

Sequence similaritiesi

Belongs to the CSN4 family.Curated
Contains 1 PCI domain.Curated

Phylogenomic databases

eggNOGiKOG1497. Eukaryota.
ENOG410XPDE. LUCA.
GeneTreeiENSGT00730000111161.
HOGENOMiHOG000158382.
HOVERGENiHBG051136.
InParanoidiQ9BT78.
KOiK12178.
PhylomeDBiQ9BT78.
TreeFamiTF101147.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR000717. PCI_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF01399. PCI. 1 hit.
[Graphical view]
SMARTiSM00088. PINT. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BT78-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAAAVRQDLA QLMNSSGSHK DLAGKYRQIL EKAIQLSGAE QLEALKAFVE
60 70 80 90 100
AMVNENVSLV ISRQLLTDFC THLPNLPDST AKEIYHFTLE KIQPRVISFE
110 120 130 140 150
EQVASIRQHL ASIYEKEEDW RNAAQVLVGI PLETGQKQYN VDYKLETYLK
160 170 180 190 200
IARLYLEDDD PVQAEAYINR ASLLQNESTN EQLQIHYKVC YARVLDYRRK
210 220 230 240 250
FIEAAQRYNE LSYKTIVHES ERLEALKHAL HCTILASAGQ QRSRMLATLF
260 270 280 290 300
KDERCQQLAA YGILEKMYLD RIIRGNQLQE FAAMLMPHQK ATTADGSSIL
310 320 330 340 350
DRAVIEHNLL SASKLYNNIT FEELGALLEI PAAKAEKIAS QMITEGRMNG
360 370 380 390 400
FIDQIDGIVH FETREALPTW DKQIQSLCFQ VNNLLEKISQ TAPEWTAQAM

EAQMAQ
Length:406
Mass (Da):46,269
Last modified:June 1, 2001 - v1
Checksum:i4EFF9079058EB609
GO
Isoform 2 (identifier: Q9BT78-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     335-406: AEKIASQMIT...AQAMEAQMAQ → HEKPCQRGISRSNHFVSK

Note: No experimental confirmation available.
Show »
Length:352
Mass (Da):40,197
Checksum:i40236068B86EDB52
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti2Missing in AAD43021 (Ref. 1) Curated1
Sequence conflicti97I → V in BAA91555 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_046336335 – 406AEKIA…AQMAQ → HEKPCQRGISRSNHFVSK in isoform 2. 1 PublicationAdd BLAST72

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF100757 mRNA. Translation: AAD43021.1.
AK001210 mRNA. Translation: BAA91555.1.
AK024005 mRNA. Translation: BAG51250.1.
AK094238 mRNA. Translation: BAG52847.1.
AC021105 Genomic DNA. No translation available.
AC073840 Genomic DNA. No translation available.
AC108473 Genomic DNA. No translation available.
CH471057 Genomic DNA. Translation: EAX05921.1.
CH471057 Genomic DNA. Translation: EAX05922.1.
BC004302 mRNA. Translation: AAH04302.1.
BC009292 mRNA. Translation: AAH09292.1.
BC093007 mRNA. Translation: AAH93007.1.
CCDSiCCDS3600.1. [Q9BT78-1]
CCDS58909.1. [Q9BT78-2]
RefSeqiNP_001244935.1. NM_001258006.1. [Q9BT78-2]
NP_001317656.1. NM_001330727.1.
NP_057213.2. NM_016129.2. [Q9BT78-1]
UniGeneiHs.190384.

Genome annotation databases

EnsembliENST00000264389; ENSP00000264389; ENSG00000138663. [Q9BT78-1]
ENST00000509093; ENSP00000425976; ENSG00000138663. [Q9BT78-2]
GeneIDi51138.
KEGGihsa:51138.
UCSCiuc003hoa.4. human. [Q9BT78-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF100757 mRNA. Translation: AAD43021.1.
AK001210 mRNA. Translation: BAA91555.1.
AK024005 mRNA. Translation: BAG51250.1.
AK094238 mRNA. Translation: BAG52847.1.
AC021105 Genomic DNA. No translation available.
AC073840 Genomic DNA. No translation available.
AC108473 Genomic DNA. No translation available.
CH471057 Genomic DNA. Translation: EAX05921.1.
CH471057 Genomic DNA. Translation: EAX05922.1.
BC004302 mRNA. Translation: AAH04302.1.
BC009292 mRNA. Translation: AAH09292.1.
BC093007 mRNA. Translation: AAH93007.1.
CCDSiCCDS3600.1. [Q9BT78-1]
CCDS58909.1. [Q9BT78-2]
RefSeqiNP_001244935.1. NM_001258006.1. [Q9BT78-2]
NP_001317656.1. NM_001330727.1.
NP_057213.2. NM_016129.2. [Q9BT78-1]
UniGeneiHs.190384.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4D0PX-ray1.60A1-363[»]
4D10X-ray3.80D/L1-406[»]
4D18X-ray4.08D/L1-406[»]
4WSNX-ray5.50D/L/T/b/j/r1-406[»]
ProteinModelPortaliQ9BT78.
SMRiQ9BT78.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119324. 97 interactors.
DIPiDIP-34516N.
IntActiQ9BT78. 29 interactors.
MINTiMINT-1464138.
STRINGi9606.ENSP00000264389.

PTM databases

iPTMnetiQ9BT78.
PhosphoSitePlusiQ9BT78.
SwissPalmiQ9BT78.

Polymorphism and mutation databases

BioMutaiCOPS4.
DMDMi55976582.

2D gel databases

OGPiQ9BT78.
REPRODUCTION-2DPAGEIPI00171844.

Proteomic databases

EPDiQ9BT78.
MaxQBiQ9BT78.
PaxDbiQ9BT78.
PeptideAtlasiQ9BT78.
PRIDEiQ9BT78.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000264389; ENSP00000264389; ENSG00000138663. [Q9BT78-1]
ENST00000509093; ENSP00000425976; ENSG00000138663. [Q9BT78-2]
GeneIDi51138.
KEGGihsa:51138.
UCSCiuc003hoa.4. human. [Q9BT78-1]

Organism-specific databases

CTDi51138.
DisGeNETi51138.
GeneCardsiCOPS4.
HGNCiHGNC:16702. COPS4.
HPAiHPA036894.
HPA042828.
MIMi616008. gene.
neXtProtiNX_Q9BT78.
OpenTargetsiENSG00000138663.
PharmGKBiPA26756.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1497. Eukaryota.
ENOG410XPDE. LUCA.
GeneTreeiENSGT00730000111161.
HOGENOMiHOG000158382.
HOVERGENiHBG051136.
InParanoidiQ9BT78.
KOiK12178.
PhylomeDBiQ9BT78.
TreeFamiTF101147.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000138663-MONOMER.
ReactomeiR-HSA-5696394. DNA Damage Recognition in GG-NER.
R-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-8856825. Cargo recognition for clathrin-mediated endocytosis.

Miscellaneous databases

ChiTaRSiCOPS4. human.
GeneWikiiCOPS4.
GenomeRNAii51138.
PROiQ9BT78.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000138663.
CleanExiHS_COPS4.
ExpressionAtlasiQ9BT78. baseline and differential.
GenevisibleiQ9BT78. HS.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR000717. PCI_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF01399. PCI. 1 hit.
[Graphical view]
SMARTiSM00088. PINT. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCSN4_HUMAN
AccessioniPrimary (citable) accession number: Q9BT78
Secondary accession number(s): B3KN88
, B3KST5, Q561W7, Q9NW31, Q9Y677
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: June 1, 2001
Last modified: November 30, 2016
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.