Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
FSCOP2B SuperfamilyJAB1/MPN domain-like8053244 3001105 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyEIF3 subunit F C-terminal domain-like8053243 3002167 SCOP2B (2022-06-29)
J [auth P]SCOP2B SuperfamilyUbiquitin-like8038575 3000157 SCOP2B (2022-06-29)
M [auth R]SCOP2B SuperfamilyRING/U-box like8040866 3000160 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyWinged helix DNA-binding domain8057039 3000034 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyTPR-like8057037 3001345 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyTPR-like8057036 3001345 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyUbiquitin-like8034470 3000157 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyJAB1/MPN domain-like8053263 3001105 SCOP2B (2022-06-29)
I [auth V]SCOP2B SuperfamilyVHL8041313 3000841 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DPCIe6r7fD1 A: alpha arraysX: HTHH: HTHT: wingedF: PCIECOD (1.6)
DRPN7_1e6r7fD3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: RPN7_1ECOD (1.6)
DKOG1497e6r7fD2 A: extended segmentsX: 26S proteasome regulatory subunits C-terminal helicesH: 26S proteasome regulatory subunit RPN5 C-terminal helix (From Topology)T: 26S proteasome regulatory subunit RPN5 C-terminal helixF: KOG1497ECOD (1.6)
FJAB_1e6r7fF1 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: JAB_1ECOD (1.6)
FMitMem_rege6r7fF2 A: extended segmentsX: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)H: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)T: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domainF: MitMem_regECOD (1.6)
J [auth P]ubiquitin_2e6r7fP1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_2ECOD (1.6)
K [auth Q]Skp1_POZ_1e6r7fQ1 A: a+b two layersX: POZ domain (From Topology)H: POZ domain (From Topology)T: POZ domainF: Skp1_POZ_1ECOD (1.6)
M [auth R]zf-rbx1e6r7fR1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: zf-rbx1ECOD (1.6)
APCI_2e6r7fA2 A: alpha arraysX: HTHH: HTHT: wingedF: PCI_2ECOD (1.6)
ARPN7e6r7fA3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: RPN7ECOD (1.6)
AKOG0686_2nde6r7fA1 A: extended segmentsX: 26S proteasome regulatory subunits C-terminal helicesH: 26S proteasome regulatory subunit RPN7 C-terminal helix (From Topology)T: 26S proteasome regulatory subunit RPN7 C-terminal helixF: KOG0686_2ndECOD (1.6)
L [auth O]Cullin_Nedd8e6r7fO3 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_Nedd8ECOD (1.6)
L [auth O]Cullin_4the6r7fO1 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_4thECOD (1.6)
L [auth O]Cullin_1ste6r7fO5 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_1stECOD (1.6)
L [auth O]Cullin_2nde6r7fO4 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_2ndECOD (1.6)
L [auth O]Cullin_3rde6r7fO2 A: a+b duplicates or obligate multimersX: a+b domain in cullin-like proteins (From Topology)H: a+b domain in cullin-like proteins (From Topology)T: a+b domain in cullin-like proteinsF: Cullin_3rdECOD (1.6)
Nubiquitin_4e6r7fN1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_4ECOD (1.6)
BPCI_1e6r7fB1 A: alpha arraysX: HTHH: HTHT: wingedF: PCI_1ECOD (1.6)
BKOG2581e6r7fB3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: KOG2581ECOD (1.6)
BKOG1464e6r7fB2 A: extended segmentsX: 26S proteasome regulatory subunits C-terminal helicesH: 26S proteasome regulatory subunit RPN9 C-terminal helix (From Topology)T: 26S proteasome regulatory subunit RPN9 C-terminal helixF: KOG1464ECOD (1.6)
CPCI,KOG2581e6r7fC1 A: alpha arraysX: HTHH: HTHT: wingedF: PCI,KOG2581ECOD (1.6)
CKOG2581e6r7fC3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: KOG2581ECOD (1.6)
CKOG2582_likee6r7fC2 A: extended segmentsX: 26S proteasome regulatory subunits C-terminal helicesH: 26S proteasome regulatory subunit RPN3 C-terminal helix (From Topology)T: 26S proteasome regulatory subunit RPN3 C-terminal helixF: KOG2582_likeECOD (1.6)
EJABe6r7fE1 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: JABECOD (1.6)
EKOG1554e6r7fE2 A: extended segmentsX: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)H: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)T: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domainF: KOG1554ECOD (1.6)
G [auth H]CSN8_PSD8_EIF3K_C_1e6r7fH1 A: alpha arraysX: HTHH: HTHT: wingedF: CSN8_PSD8_EIF3K_C_1ECOD (1.6)
G [auth H]CSN8_PSD8_EIF3K_Ne6r7fH2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: CSN8_PSD8_EIF3K_NECOD (1.6)
H [auth G]PCIe6r7fG2 A: alpha arraysX: HTHH: HTHT: wingedF: PCIECOD (1.6)
H [auth G]KOG3250_1ste6r7fG1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: KOG3250_1stECOD (1.6)
H [auth G]KOG3250_2nde6r7fG3 A: extended segmentsX: 26S proteasome regulatory subunits C-terminal helicesH: 26S proteasome regulatory subunit RPN9 C-terminal helix (From Topology)T: 26S proteasome regulatory subunit RPN9 C-terminal helixF: KOG3250_2ndECOD (1.6)
I [auth V]VHLe6r7fV2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Prealbumin-likeF: VHLECOD (1.6)
I [auth V]VHL_Ce6r7fV1 A: alpha arraysX: SOCS box-like (From Topology)H: SOCS box-like (From Topology)T: SOCS box-likeF: VHL_CECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF18420CSN4/RPN5/eIF3a helix turn helix domain (CSN4_RPN5_eIF3a)CSN4/RPN5/eIF3a helix turn helix domainCullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). Enzymatically, CSN functions as an isopeptidase that removes the ubiquitin-like activator NEDD8 from CRLs, but it can also bind deneddylated CRLs and m ...Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). Enzymatically, CSN functions as an isopeptidase that removes the ubiquitin-like activator NEDD8 from CRLs, but it can also bind deneddylated CRLs and maintain them in an inactive state. The CSN subunits CSN1, CSN2, CSN3, CSN4, CSN7 and CSN8, share a common domain composition: an N-terminal array of tandem alpha-helical tetratricopeptide/-like repeats, a 34 residue motif, followed by a PCI domain, which encompasses a WH subdomain, a linker, and one or two alpha-helices at the C-terminus. This entry describes the C-terminal helices found on CSN4. The two helices from CSN4 (helices I and II) form a brace roughly perpendicular to the bundle axis in contact with the three C-terminal helices of CSN6. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Both CSN1 and CSN4 are dependent on the presence of their C-terminal helix (CSN1 isoform-2 residues: 466-527; and CSN4: 364-406) for integration into CSN. COP9 signalosome shares common architecture with the 26S proteasome lid and eIF3 where the 19S lid subunit RPN5 and the eIF3 core subunit eIF3a share significant structural similarity with CSN4 [1].
Domain
PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].Domain
PF13012Maintenance of mitochondrial structure and function (MitMem_reg)Maintenance of mitochondrial structure and function- Family
PF01398JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)JAB1/Mov34/MPN/PAD-1 ubiquitin protease- Family
J [auth P]PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
K [auth Q]PF03931Skp1 family, tetramerisation domain (Skp1_POZ)Skp1 family, tetramerisation domain- Domain
M [auth R]PF12678RING-H2 zinc finger domain (zf-rbx1)RING-H2 zinc finger domainThere are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell ...There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control [1].
Domain
PF21151COP9 signalosome complex subunit 1, C-terminal helix (CSN1_C)COP9 signalosome complex subunit 1, C-terminal helixThis is the C-terminal helix from COP9 signalosome complex subunit 1, an essential component of the COP9 signalosome complex (CSN), which involved in various cellular and developmental processes [1,2].Domain
PF1060226S proteasome subunit RPN7 (RPN7)26S proteasome subunit RPN7- Repeat
PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].Domain
L [auth O]PF00888Cullin family (Cullin)Cullin family- Repeat
L [auth O]PF10557Cullin protein neddylation domain (Cullin_Nedd8)Cullin protein neddylation domainThis is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cu ...This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue [1].
Domain
PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].Domain
PF21215COP9 signalosome complex subunit 3-like, C-terminal helix (CSN3-like_C)COP9 signalosome complex subunit 3-like, C-terminal helixThis domain is found in COP9 signalosome complex subunit 3 from humans (CSN3) and similar proteins predominantly found in vertebrates. CSN3 is a component of the eight-subunit COP9 signalosome complex (CSN), which inactivate Cullin-RING E3 ubiquitin ...This domain is found in COP9 signalosome complex subunit 3 from humans (CSN3) and similar proteins predominantly found in vertebrates. CSN3 is a component of the eight-subunit COP9 signalosome complex (CSN), which inactivate Cullin-RING E3 ubiquitin ligases (CRLs) by removing their covalently attached activator, NEDD8. This entry represents the C-terminal helical decoration of this protein [1,2].
Domain
PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].Domain
PF18323Cop9 signalosome subunit 5 C-terminal domain (CSN5_C)Cop9 signalosome subunit 5 C-terminal domainThe COP9 (Constitutive photomorphogenesis 9) signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs) [1]. The catalytic ac ...The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs) [1]. The catalytic activity of the CSN complex is carried by subunit 5 (CSN5), also known as c-Jun activation domain-binding protein-1 (Jab1) [1]. This entry is the C-terminal domain found in CSN5 proteins. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Deletion of the C-terminal helices has a pronounced effect on CSN integrity [2].
Domain
PF01398JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)JAB1/Mov34/MPN/PAD-1 ubiquitin protease- Family
H [auth G]PF18392COP9 signalosome complex subunit 7a helix I domain (CSN7a_helixI)COP9 signalosome complex subunit 7a helix I domainThis is The C-terminal helix I domain found in COP9 signalosome complex subunit 7a. The helix from CSN7 (helix I) contacts CSN6 helices I and II at the base of the bundle, nearest the PCI ring [1].Domain
H [auth G]PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].Domain
I [auth V]PF17211VHL box domain (VHL_C)VHL box domainThis domain represents the short C-terminal alpha helical domain from the VHL protein [1].Domain
I [auth V]PF01847VHL beta domain (VHL)VHL beta domainVHL forms a ternary complex with the elonginB Swiss:O44226 and elonginC Swiss:O13292 proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor Swiss:P15692 mRNA.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
COP9 signalosome complex subunit 4
COP9 signalosome complex subunit 6-
J [auth P]Elongin-B
K [auth Q]Elongin-C
M [auth R]E3 ubiquitin-protein ligase RBX1
COP9 signalosome complex subunit 1
L [auth O]Cullin-2
NEDD8
COP9 signalosome complex subunit 2
COP9 signalosome complex subunit 3-
COP9 signalosome complex subunit 5
G [auth H]COP9 signalosome complex subunit 8-
H [auth G]COP9 signalosome complex subunit 7b-
I [auth V]von Hippel-Lindau disease tumor suppressor

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR041406COP9 signalosome complex subunit 4, helix turn helix domainDomain
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
IPR000717Proteasome component (PCI) domainDomain
IPR04013426S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4Family
IPR024969EIF3F/CSN6-like, C-terminalDomain
IPR037518MPN domainDomain
IPR033859COP9 signalosome subunit 6Family
IPR000555JAB1/MPN/MOV34 metalloenzyme domainDomain
J [auth P]IPR000626Ubiquitin-like domainDomain
J [auth P]IPR039049Elongin BFamily
J [auth P]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
K [auth Q]IPR016073SKP1 component, POZ domainDomain
K [auth Q]IPR001232S-phase kinase-associated protein 1-likeFamily
K [auth Q]IPR039948Elongin-CFamily
K [auth Q]IPR011333SKP1/BTB/POZ domain superfamilyHomologous Superfamily
M [auth R]IPR024766Zinc finger, RING-H2-typeDomain
M [auth R]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
M [auth R]IPR001841Zinc finger, RING-typeDomain
IPR048624COP9 signalosome complex subunit 1, C-terminal helixDomain
IPR01958526S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1Family
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
IPR000717Proteasome component (PCI) domainDomain
IPR04513526S proteasome regulatory subunit Rpn7, N-terminalDomain
L [auth O]IPR045093CullinFamily
L [auth O]IPR019559Cullin protein, neddylation domainDomain
L [auth O]IPR016158Cullin homology domainDomain
L [auth O]IPR016157Cullin, conserved siteConserved Site
L [auth O]IPR001373Cullin, N-terminalDomain
L [auth O]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
L [auth O]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
L [auth O]IPR036317Cullin homology domain superfamilyHomologous Superfamily
L [auth O]IPR016159Cullin repeat-like-containing domain superfamilyHomologous Superfamily
IPR019954Ubiquitin conserved siteConserved Site
IPR000626Ubiquitin-like domainDomain
IPR019956Ubiquitin domainDomain
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
IPR038738Nedd8-like ubiquitinDomain
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
IPR000717Proteasome component (PCI) domainDomain
IPR048621COP9 signalosome complex subunit 3, C-terminal helixDomain
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
IPR000717Proteasome component (PCI) domainDomain
IPR040961Cop9 signalosome subunit 5 C-terminal domainDomain
IPR037518MPN domainDomain
IPR000555JAB1/MPN/MOV34 metalloenzyme domainDomain
G [auth H]IPR033205COP9 signalosome, subunit CSN8Family
G [auth H]IPR033464CSN8/PSMD8/EIF3KDomain
G [auth H]IPR000717Proteasome component (PCI) domainDomain
H [auth G]IPR045237Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7Family
H [auth G]IPR041481COP9 signalosome complex subunit 7, helix IDomain
H [auth G]IPR000717Proteasome component (PCI) domainDomain
I [auth V]IPR037139von Hippel-Lindau disease tumour suppressor, alpha domain superfamilyHomologous Superfamily
I [auth V]IPR022772von Hippel-Lindau disease tumour suppressor, beta/alpha domainDomain
I [auth V]IPR024053von Hippel-Lindau disease tumour suppressor, beta domainDomain
I [auth V]IPR024048von Hippel-Lindau disease tumour suppressor, alpha domainDomain
I [auth V]IPR036208VHL superfamilyHomologous Superfamily
I [auth V]IPR037140von Hippel-Lindau disease tumour suppressor, beta domain superfamilyHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
PharosQ9BT78
PharosQ7L5N1
J [auth P]PharosQ15370
K [auth Q]PharosQ15369
M [auth R]PharosP62877
PharosQ13098
L [auth O]PharosQ13617
PharosQ15843
PharosP61201
PharosQ9UNS2
PharosQ92905
G [auth H]PharosQ99627
H [auth G]PharosQ9H9Q2
I [auth V]PharosP40337