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Conserved domains on  [gi|8918353|dbj|BAA97581|]
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pUb-R5 [Homo sapiens]

Protein Classification

26S proteasome non-ATPase regulatory subunit 4( domain architecture ID 10106897)

26S proteasome non-ATPase regulatory subunit 4 is a component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VWA_26S_proteasome_subunit cd01452
26S proteasome plays a major role in eukaryotic protein breakdown, especially for ...
 1-187 1.80e-121

26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.


:

Pssm-ID: 238729  Cd Length: 187  Bit Score: 344.35  E-value: 1.80e-121
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    1 MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLAND-CEVLTTLTPDTGRILSKLHTVQ 79
Cdd:cd01452   1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNsPEVLVTLTNDQGKILSKLHDVQ 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353   80 PKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNT 159
Cdd:cd01452  81 PKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160

                       170       180
                ....*....|....*....|....*....
gi 8918353  160 LNGKDgtGSHLVTVPPGPSLA-DALISSP 187
Cdd:cd01452 161 VNGKD--GSHLVSVPPGENLLsDALLSSP 187
 
Name Accession Description Interval E-value
VWA_26S_proteasome_subunit cd01452
26S proteasome plays a major role in eukaryotic protein breakdown, especially for ...
 1-187 1.80e-121

26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.


Pssm-ID: 238729  Cd Length: 187  Bit Score: 344.35  E-value: 1.80e-121
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    1 MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLAND-CEVLTTLTPDTGRILSKLHTVQ 79
Cdd:cd01452   1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNsPEVLVTLTNDQGKILSKLHDVQ 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353   80 PKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNT 159
Cdd:cd01452  81 PKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160

                       170       180
                ....*....|....*....|....*....
gi 8918353  160 LNGKDgtGSHLVTVPPGPSLA-DALISSP 187
Cdd:cd01452 161 VNGKD--GSHLVSVPPGENLLsDALLSSP 187
VWA_2 pfam13519
von Willebrand factor type A domain;
6-112 2.13e-28

von Willebrand factor type A domain;


Pssm-ID: 463909 [Multi-domain]  Cd Length: 103  Bit Score: 104.30  E-value: 2.13e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353      6 TMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHsktrSNPENNVGLITLANDCEVLTTLTPDTGRILSKLHTVQPKGKIT 85
Cdd:pfam13519   1 LVFVLDTSGSMRNGDYGPTRLEAAKDAVLALLK----SLPGDRVGLVTFGDGPEVLIPLTKDRAKILRALRRLEPKGGGT 76

                          90       100
                  ....*....|....*....|....*...
gi 8918353     86 -FCTGIRVAHLALKHRQgKNHKMRIIAF 112
Cdd:pfam13519  77 nLAAALQLARAALKHRR-KNQPRRIVLI 103
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
 7-187 3.52e-16

von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.


Pssm-ID: 214621 [Multi-domain]  Cd Length: 175  Bit Score: 74.03  E-value: 3.52e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353       7 MVCVDNSEYMRngdflPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEVLTTL--TPDTGRILSKLHTVQPK-GK 83
Cdd:smart00327   3 VFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDARVLFPLndSRSKDALLEALASLSYKlGG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353      84 IT-FCTGIRVAHLALKHRQGKNHKMR---IIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGeeevnTEKLTAFVNT 159
Cdd:smart00327  78 GTnLGAALQYALENLFSKSAGSRRGApkvVILITDGESNDGPKDLLKAAKELKRSGVKVFVVGVG-----NDVDEEELKK 152

                          170       180
                   ....*....|....*....|....*...
gi 8918353     160 LNGKDGTGSHLVtvppgPSLADALISSP 187
Cdd:smart00327 153 LASAPGGVYVFL-----PELLDLLIDLL 175
PRK13685 PRK13685
hypothetical protein; Provisional
 7-67 4.02e-03

hypothetical protein; Provisional


Pssm-ID: 184242 [Multi-domain]  Cd Length: 326  Bit Score: 38.14  E-value: 4.02e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 8918353     7 MVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTrsnPENNVGLITLANDCEVLTTLTPD 67
Cdd:PRK13685  92 MLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELT---PGINLGLIAFAGTATVLVSPTTN 149
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 2-146 6.78e-03

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227480 [Multi-domain]  Cd Length: 421  Bit Score: 37.67  E-value: 6.78e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    2 VLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEVLTT-LTPDTGRILSKLHTV-Q 79
Cdd:COG5151  86 IIRHLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCAKYTSsMDGNPQAHIGQLKSKrD 165

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 8918353   80 PKGKITFCTGIRVAHLALKHRqgKNHKMR-IIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEE 146
Cdd:COG5151 166 CSGNFSLQNALEMARIELMKN--TMHGTReVLIIFGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAE 231
 
Name Accession Description Interval E-value
VWA_26S_proteasome_subunit cd01452
26S proteasome plays a major role in eukaryotic protein breakdown, especially for ...
 1-187 1.80e-121

26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.


Pssm-ID: 238729  Cd Length: 187  Bit Score: 344.35  E-value: 1.80e-121
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    1 MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLAND-CEVLTTLTPDTGRILSKLHTVQ 79
Cdd:cd01452   1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNsPEVLVTLTNDQGKILSKLHDVQ 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353   80 PKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNT 159
Cdd:cd01452  81 PKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160

                       170       180
                ....*....|....*....|....*....
gi 8918353  160 LNGKDgtGSHLVTVPPGPSLA-DALISSP 187
Cdd:cd01452 161 VNGKD--GSHLVSVPPGENLLsDALLSSP 187
VWA_2 pfam13519
von Willebrand factor type A domain;
6-112 2.13e-28

von Willebrand factor type A domain;


Pssm-ID: 463909 [Multi-domain]  Cd Length: 103  Bit Score: 104.30  E-value: 2.13e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353      6 TMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHsktrSNPENNVGLITLANDCEVLTTLTPDTGRILSKLHTVQPKGKIT 85
Cdd:pfam13519   1 LVFVLDTSGSMRNGDYGPTRLEAAKDAVLALLK----SLPGDRVGLVTFGDGPEVLIPLTKDRAKILRALRRLEPKGGGT 76

                          90       100
                  ....*....|....*....|....*...
gi 8918353     86 -FCTGIRVAHLALKHRQgKNHKMRIIAF 112
Cdd:pfam13519  77 nLAAALQLARAALKHRR-KNQPRRIVLI 103
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
 7-187 3.52e-16

von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.


Pssm-ID: 214621 [Multi-domain]  Cd Length: 175  Bit Score: 74.03  E-value: 3.52e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353       7 MVCVDNSEYMRngdflPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEVLTTL--TPDTGRILSKLHTVQPK-GK 83
Cdd:smart00327   3 VFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDARVLFPLndSRSKDALLEALASLSYKlGG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353      84 IT-FCTGIRVAHLALKHRQGKNHKMR---IIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGeeevnTEKLTAFVNT 159
Cdd:smart00327  78 GTnLGAALQYALENLFSKSAGSRRGApkvVILITDGESNDGPKDLLKAAKELKRSGVKVFVVGVG-----NDVDEEELKK 152

                          170       180
                   ....*....|....*....|....*...
gi 8918353     160 LNGKDGTGSHLVtvppgPSLADALISSP 187
Cdd:smart00327 153 LASAPGGVYVFL-----PELLDLLIDLL 175
vWFA cd00198
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
 7-162 7.66e-10

Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.


Pssm-ID: 238119 [Multi-domain]  Cd Length: 161  Bit Score: 56.42  E-value: 7.66e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    7 MVCVDNSEYMRngdflPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEVLTTLTPDTG-----RILSKLHTvQPK 81
Cdd:cd00198   4 VFLLDVSGSMG-----GEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLTTDTDkadllEAIDALKK-GLG 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353   82 GKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGeEEVNTEKLTAFVNTLN 161
Cdd:cd00198  78 GGTNIGAALRLALELLKSAKRPNARRVIILLTDGEPNDGPELLAEAARELRKLGITVYTIGIG-DDANEDELKEIADKTT 156


                .
gi 8918353  162 G 162
Cdd:cd00198 157 G 157
vWA_transcription_factor_IIH_type cd01453
Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five ...
 7-141 3.08e-07

Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.


Pssm-ID: 238730  Cd Length: 183  Bit Score: 49.25  E-value: 3.08e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    7 MVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDC-EVLTTLTPDTGRILSKLHTVQ-PKGKI 84
Cdd:cd01453   7 IIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRaEKLTDLTGNPRKHIQALKTAReCSGEP 86

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 8918353   85 TFCTGIRVAHLALKHRQGKNHKMRIIAFvGSPVEDNEKDLVKLAKRLKKEKVNVDII 141
Cdd:cd01453  87 SLQNGLEMALESLKHMPSHGSREVLIIF-SSLSTCDPGNIYETIDKLKKENIRVSVI 142
VWA pfam00092
von Willebrand factor type A domain;
10-145 1.75e-03

von Willebrand factor type A domain;


Pssm-ID: 459670 [Multi-domain]  Cd Length: 174  Bit Score: 38.41  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353     10 VDNSEYMRNGDFLptrlQAQQDAVNIVchSK-TRSNPENNVGLITLANDCEVLTTLTPDTGR--ILSKLHTVQPKGKITF 86
Cdd:pfam00092   6 LDGSGSIGGDNFE----KVKEFLKKLV--ESlDIGPDGTRVGLVQYSSDVRTEFPLNDYSSKeeLLSAVDNLRYLGGGTT 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 8918353     87 CTG---IRVAHLALKHRQG--KNHKMRIIAFV-GSPvedNEKDLVKLAKRLKKEKVNVDIINFGE 145
Cdd:pfam00092  80 NTGkalKYALENLFSSAAGarPGAPKVVVLLTdGRS---QDGDPEEVARELKSAGVTVFAVGVGN 141
PRK13685 PRK13685
hypothetical protein; Provisional
 7-67 4.02e-03

hypothetical protein; Provisional


Pssm-ID: 184242 [Multi-domain]  Cd Length: 326  Bit Score: 38.14  E-value: 4.02e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 8918353     7 MVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTrsnPENNVGLITLANDCEVLTTLTPD 67
Cdd:PRK13685  92 MLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELT---PGINLGLIAFAGTATVLVSPTTN 149
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 2-146 6.78e-03

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227480 [Multi-domain]  Cd Length: 421  Bit Score: 37.67  E-value: 6.78e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8918353    2 VLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEVLTT-LTPDTGRILSKLHTV-Q 79
Cdd:COG5151  86 IIRHLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCAKYTSsMDGNPQAHIGQLKSKrD 165

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 8918353   80 PKGKITFCTGIRVAHLALKHRqgKNHKMR-IIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEE 146
Cdd:COG5151 166 CSGNFSLQNALEMARIELMKN--TMHGTReVLIIFGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAE 231
 
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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