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Conserved domains on  [gi|38373690|ref|NP_057213|]
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COP9 signalosome complex subunit 4 isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSN4_RPN5_eIF3a pfam18420
CSN4/RPN5/eIF3a helix turn helix domain; Cullin-RING E3 ubiquitin ligases (CRLs) are regulated ...
 365-406 3.93e-21

CSN4/RPN5/eIF3a helix turn helix domain; 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.


:

Pssm-ID: 375846  Cd Length: 42  Bit Score: 85.47  E-value: 3.93e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 38373690   365 EALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ 406
Cdd:pfam18420   1 EVLPTWDKQIQSLCYQVNNLIEKISQAEPEWMAKAMEEQMTQ 42
PCI pfam01399
PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and ...
 264-362 1.81e-19

PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).


:

Pssm-ID: 460195  Cd Length: 105  Bit Score: 83.04  E-value: 1.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690   264 LEKMYLDRIIRGNQLQEFAAMLMPHQKAT-----TADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKI 338
Cdd:pfam01399   1 PAYRDLLRAFYSGDLSEFEEILADYKEELllddgLAEHLEDLRRKIREHNLRQLSKPYSSISLSDLAKLLGLSVDEVEKI 80

                          90       100
                  ....*....|....*....|....
gi 38373690   339 ASQMITEGRMNGFIDQIDGIVHFE 362
Cdd:pfam01399  81 LAKLIRDGRIRAKIDQVNGIVVFS 104
RPN5 super family cl21585
26S proteasome regulatory complex component [Posttranslational modification, protein turnover, ...
 71-377 1.89e-15

26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones];


The actual alignment was detected with superfamily member COG5071:

Pssm-ID: 227403 [Multi-domain]  Cd Length: 439  Bit Score: 77.68  E-value: 1.89e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690  71 THLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETgQKQYNVDYKLETYLK 150
Cdd:COG5071  98 EYLKGIDDLKTKINLIETLRTVTEGKIFVEVERARLTQLLSQIKEEQGDIKSAQDILCNEPVET-YGSFDLSEKVAFILE 176

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 151 IARLYLEDDDPVQAEAY---INRASLLQNEStnEQLQIHYKVCYARVLDYRRKFIEAAQRYNELsYKTIVHESERL---E 224
Cdd:COG5071 177 QVRLFLLRSDYYMASTYtkkINKKFFEKEDV--QSLKLKYYELKVRIGLHDRAYLDVCKYYRAV-YDTAVVQEDPAkwkE 253

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 225 ALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYL-DRIIRGNQLQE-FAAMLMPHQKATTADGSSI--- 299
Cdd:COG5071 254 VLSNVVCFALLTPYDNEQADLLHKINADHKLNSLPLLQQLVKCFIvNELMRWPKVAEiYGSALRSNVFAFNDEKGEKrws 333

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 300 -LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETR----EALPTWDKQI 374
Cdd:COG5071 334 dLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSqnvqEQLNEWGSNV 413


                ...
gi 38373690 375 QSL 377
Cdd:COG5071 414 TEL 416
 
Name Accession Description Interval E-value
CSN4_RPN5_eIF3a pfam18420
CSN4/RPN5/eIF3a helix turn helix domain; Cullin-RING E3 ubiquitin ligases (CRLs) are regulated ...
 365-406 3.93e-21

CSN4/RPN5/eIF3a helix turn helix domain; 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.


Pssm-ID: 375846  Cd Length: 42  Bit Score: 85.47  E-value: 3.93e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 38373690   365 EALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ 406
Cdd:pfam18420   1 EVLPTWDKQIQSLCYQVNNLIEKISQAEPEWMAKAMEEQMTQ 42
PCI pfam01399
PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and ...
 264-362 1.81e-19

PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).


Pssm-ID: 460195  Cd Length: 105  Bit Score: 83.04  E-value: 1.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690   264 LEKMYLDRIIRGNQLQEFAAMLMPHQKAT-----TADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKI 338
Cdd:pfam01399   1 PAYRDLLRAFYSGDLSEFEEILADYKEELllddgLAEHLEDLRRKIREHNLRQLSKPYSSISLSDLAKLLGLSVDEVEKI 80

                          90       100
                  ....*....|....*....|....
gi 38373690   339 ASQMITEGRMNGFIDQIDGIVHFE 362
Cdd:pfam01399  81 LAKLIRDGRIRAKIDQVNGIVVFS 104
RPN5 COG5071
26S proteasome regulatory complex component [Posttranslational modification, protein turnover, ...
 71-377 1.89e-15

26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227403 [Multi-domain]  Cd Length: 439  Bit Score: 77.68  E-value: 1.89e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690  71 THLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETgQKQYNVDYKLETYLK 150
Cdd:COG5071  98 EYLKGIDDLKTKINLIETLRTVTEGKIFVEVERARLTQLLSQIKEEQGDIKSAQDILCNEPVET-YGSFDLSEKVAFILE 176

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 151 IARLYLEDDDPVQAEAY---INRASLLQNEStnEQLQIHYKVCYARVLDYRRKFIEAAQRYNELsYKTIVHESERL---E 224
Cdd:COG5071 177 QVRLFLLRSDYYMASTYtkkINKKFFEKEDV--QSLKLKYYELKVRIGLHDRAYLDVCKYYRAV-YDTAVVQEDPAkwkE 253

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 225 ALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYL-DRIIRGNQLQE-FAAMLMPHQKATTADGSSI--- 299
Cdd:COG5071 254 VLSNVVCFALLTPYDNEQADLLHKINADHKLNSLPLLQQLVKCFIvNELMRWPKVAEiYGSALRSNVFAFNDEKGEKrws 333

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 300 -LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETR----EALPTWDKQI 374
Cdd:COG5071 334 dLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSqnvqEQLNEWGSNV 413


                ...
gi 38373690 375 QSL 377
Cdd:COG5071 414 TEL 416
PINT smart00088
motif in proteasome subunits, Int-6, Nip-1 and TRIP-15; Also called the PCI (Proteasome, COP9, ...
 297-377 1.97e-13

motif in proteasome subunits, Int-6, Nip-1 and TRIP-15; Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.


Pssm-ID: 214509 [Multi-domain]  Cd Length: 88  Bit Score: 65.34  E-value: 1.97e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690    297 SSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFE-----TREALPTWD 371
Cdd:smart00088   3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEevdprRSEPLAQFA 82


                   ....*.
gi 38373690    372 KQIQSL 377
Cdd:smart00088  83 ETLKKL 88
 
Name Accession Description Interval E-value
CSN4_RPN5_eIF3a pfam18420
CSN4/RPN5/eIF3a helix turn helix domain; Cullin-RING E3 ubiquitin ligases (CRLs) are regulated ...
 365-406 3.93e-21

CSN4/RPN5/eIF3a helix turn helix domain; 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.


Pssm-ID: 375846  Cd Length: 42  Bit Score: 85.47  E-value: 3.93e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 38373690   365 EALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ 406
Cdd:pfam18420   1 EVLPTWDKQIQSLCYQVNNLIEKISQAEPEWMAKAMEEQMTQ 42
PCI pfam01399
PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and ...
 264-362 1.81e-19

PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).


Pssm-ID: 460195  Cd Length: 105  Bit Score: 83.04  E-value: 1.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690   264 LEKMYLDRIIRGNQLQEFAAMLMPHQKAT-----TADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKI 338
Cdd:pfam01399   1 PAYRDLLRAFYSGDLSEFEEILADYKEELllddgLAEHLEDLRRKIREHNLRQLSKPYSSISLSDLAKLLGLSVDEVEKI 80

                          90       100
                  ....*....|....*....|....
gi 38373690   339 ASQMITEGRMNGFIDQIDGIVHFE 362
Cdd:pfam01399  81 LAKLIRDGRIRAKIDQVNGIVVFS 104
RPN5 COG5071
26S proteasome regulatory complex component [Posttranslational modification, protein turnover, ...
 71-377 1.89e-15

26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227403 [Multi-domain]  Cd Length: 439  Bit Score: 77.68  E-value: 1.89e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690  71 THLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETgQKQYNVDYKLETYLK 150
Cdd:COG5071  98 EYLKGIDDLKTKINLIETLRTVTEGKIFVEVERARLTQLLSQIKEEQGDIKSAQDILCNEPVET-YGSFDLSEKVAFILE 176

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 151 IARLYLEDDDPVQAEAY---INRASLLQNEStnEQLQIHYKVCYARVLDYRRKFIEAAQRYNELsYKTIVHESERL---E 224
Cdd:COG5071 177 QVRLFLLRSDYYMASTYtkkINKKFFEKEDV--QSLKLKYYELKVRIGLHDRAYLDVCKYYRAV-YDTAVVQEDPAkwkE 253

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 225 ALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYL-DRIIRGNQLQE-FAAMLMPHQKATTADGSSI--- 299
Cdd:COG5071 254 VLSNVVCFALLTPYDNEQADLLHKINADHKLNSLPLLQQLVKCFIvNELMRWPKVAEiYGSALRSNVFAFNDEKGEKrws 333

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690 300 -LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETR----EALPTWDKQI 374
Cdd:COG5071 334 dLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSqnvqEQLNEWGSNV 413


                ...
gi 38373690 375 QSL 377
Cdd:COG5071 414 TEL 416
PINT smart00088
motif in proteasome subunits, Int-6, Nip-1 and TRIP-15; Also called the PCI (Proteasome, COP9, ...
 297-377 1.97e-13

motif in proteasome subunits, Int-6, Nip-1 and TRIP-15; Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.


Pssm-ID: 214509 [Multi-domain]  Cd Length: 88  Bit Score: 65.34  E-value: 1.97e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38373690    297 SSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFE-----TREALPTWD 371
Cdd:smart00088   3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEevdprRSEPLAQFA 82


                   ....*.
gi 38373690    372 KQIQSL 377
Cdd:smart00088  83 ETLKKL 88
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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