6R7N | pdb_00006r7n

Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyTPR-like 8057036 3001345 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyWinged helix DNA-binding domain 8057039 3000034 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyTPR-like 8057037 3001345 SCOP2B (2022-06-29)
D [auth P]SCOP2B SuperfamilyUbiquitin-like 8038575 3000157 SCOP2B (2022-06-29)
F [auth R]SCOP2B SuperfamilyRING/U-box like 8040866 3000160 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APCI_2e6r7nA1 A: alpha arraysX: HTHH: HTHT: wingedF: PCI_2ECOD (1.6)
ARPN7e6r7nA2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: RPN7ECOD (1.6)
AKOG0686_2nde6r7nA3 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)
B [auth D]PCIe6r7nD1 A: alpha arraysX: HTHH: HTHT: wingedF: PCIECOD (1.6)
B [auth D]RPN7_1e6r7nD3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: RPN7_1ECOD (1.6)
B [auth D]KOG1497e6r7nD2 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)
C [auth H]CSN8_PSD8_EIF3K_C_1e6r7nH1 A: alpha arraysX: HTHH: HTHT: wingedF: CSN8_PSD8_EIF3K_C_1ECOD (1.6)
C [auth H]CSN8_PSD8_EIF3K_Ne6r7nH2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: CSN8_PSD8_EIF3K_NECOD (1.6)
D [auth P]ubiquitin_2e6r7nP1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_2ECOD (1.6)
E [auth Q]Skp1_POZ_1e6r7nQ1 A: a+b two layersX: POZ domain (From Topology)H: POZ domain (From Topology)T: POZ domainF: Skp1_POZ_1ECOD (1.6)
F [auth R]zf-rbx1e6r7nR1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: zf-rbx1ECOD (1.6)
G [auth C]PCI,KOG2581e6r7nC2 A: alpha arraysX: HTHH: HTHT: wingedF: PCI,KOG2581ECOD (1.6)
G [auth C]KOG2581e6r7nC3 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: KOG2581ECOD (1.6)
G [auth C]KOG2582_likee6r7nC1 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)
H [auth G]PCIe6r7nG3 A: alpha arraysX: HTHH: HTHT: wingedF: PCIECOD (1.6)
H [auth G]KOG3250_1ste6r7nG1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: KOG3250_1stECOD (1.6)
H [auth G]KOG3250_2nde6r7nG2 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 O]Cullin_Nedd8e6r7nO2 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_Nedd8ECOD (1.6)
I [auth O]Cullin_4the6r7nO3 A: alpha arraysX: HTHH: HTHT: wingedF: Cullin_4thECOD (1.6)
I [auth O]Cullin_1ste6r7nO5 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_1stECOD (1.6)
I [auth O]Cullin_2nde6r7nO1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: Cullin_2ndECOD (1.6)
I [auth O]Cullin_3rde6r7nO4 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)
J [auth B]PCI_1e6r7nB3 A: alpha arraysX: HTHH: HTHT: wingedF: PCI_1ECOD (1.6)
J [auth B]KOG2581e6r7nB2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: KOG2581ECOD (1.6)
J [auth B]KOG1464e6r7nB1 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)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1]. Domain
PF1060226S proteasome subunit RPN7 (RPN7)26S proteasome subunit RPN7- Repeat
B [auth D]PF22241PSMD12/CSN4, N-terminal (PSMD12-CSN4_N)PSMD12/CSN4, N-terminal- Repeat
B [auth D]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 ...Domain
B [auth D]PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1]. Domain
C [auth H]PF10075CSN8/PSMD8/EIF3K family (CSN8_PSD8_EIF3K)CSN8/PSMD8/EIF3K family- Family
D [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 ...Domain
E [auth Q]PF03931Skp1 family, tetramerisation domain (Skp1_POZ)Skp1 family, tetramerisation domainDomain
F [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 ...Domain
G [auth C]PF22788COP9 signalosome complex subunit 3, N-terminal helical repeats (COP9_hel_rpt)COP9 signalosome complex subunit 3, N-terminal helical repeats- Repeat
G [auth C]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 ...Domain
G [auth C]PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1]. Domain
H [auth G]PF22061CSN7 helical bundle subdomain (CSN7_HB_subdom)CSN7 helical bundle subdomain- Repeat
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
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
I [auth O]PF00888Cullin family (Cullin)Cullin family- Repeat
I [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 ...Domain
J [auth B]PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1]. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
COP9 signalosome complex subunit 1
B [auth D]COP9 signalosome complex subunit 4
C [auth H]COP9 signalosome complex subunit 8-
D [auth P]Elongin-B
E [auth Q]Elongin-C
F [auth R]RBX1 E3 ubiquitin-protein ligase
G [auth C]COP9 signalosome complex subunit 3-
H [auth G]CSN7B_HUMAN-
I [auth O]Cullin-2
J [auth B]COP9 signalosome complex subunit 2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
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
B [auth D]IPR041406COP9 signalosome complex subunit 4, helix turn helix domainDomain
B [auth D]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
B [auth D]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
B [auth D]IPR000717Proteasome component (PCI) domainDomain
B [auth D]IPR04013426S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4Family
B [auth D]IPR054559PSMD12/CSN4-like, N-terminalDomain
C [auth H]IPR033205COP9 signalosome, subunit CSN8Family
C [auth H]IPR033464CSN8/PSMD8/EIF3KDomain
C [auth H]IPR000717Proteasome component (PCI) domainDomain
D [auth P]IPR000626Ubiquitin-like domainDomain
D [auth P]IPR039049Elongin BFamily
D [auth P]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
E [auth Q]IPR016073SKP1 component, POZ domainDomain
E [auth Q]IPR001232S-phase kinase-associated protein 1-likeFamily
E [auth Q]IPR039948Elongin-CFamily
E [auth Q]IPR011333SKP1/BTB/POZ domain superfamilyHomologous Superfamily
F [auth R]IPR051031RING-box E3 Ubiquitin LigaseFamily
F [auth R]IPR024766Zinc finger, RING-H2-typeDomain
F [auth R]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
F [auth R]IPR001841Zinc finger, RING-typeDomain
G [auth C]IPR048621COP9 signalosome complex subunit 3, C-terminal helixDomain
G [auth C]IPR050756COP9 signalosome complex subunit 3Family
G [auth C]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
G [auth C]IPR055089COP9 signalosome complex subunit 3, N-terminal helical repeatsDomain
G [auth C]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 O]IPR045093CullinFamily
I [auth O]IPR019559Cullin protein, neddylation domainDomain
I [auth O]IPR016158Cullin homology domainDomain
I [auth O]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
I [auth O]IPR016157Cullin, conserved siteConserved Site
I [auth O]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
I [auth O]IPR036317Cullin homology domain superfamilyHomologous Superfamily
I [auth O]IPR001373Cullin, N-terminalDomain
I [auth O]IPR016159Cullin repeat-like-containing domain superfamilyHomologous Superfamily
J [auth B]IPR05087126S Proteasome and COP9 Signalosome ComponentsFamily
J [auth B]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
J [auth B]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
J [auth B]IPR000717Proteasome component (PCI) domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
PharosQ13098
B [auth D]PharosQ9BT78
C [auth H]PharosQ99627
D [auth P]PharosQ15370
E [auth Q]PharosQ15369
F [auth R]PharosP62877
G [auth C]PharosQ9UNS2
H [auth G]PharosQ9H9Q2
I [auth O]PharosQ13617
J [auth B]PharosP61201