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8H3R

Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0000209biological_processprotein polyubiquitination
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0006006biological_processglucose metabolic process
A0006629biological_processlipid metabolic process
A0010467biological_processgene expression
A0016567biological_processprotein ubiquitination
A0031463cellular_componentCul3-RING ubiquitin ligase complex
A0032868biological_processresponse to insulin
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0043491biological_processphosphatidylinositol 3-kinase/protein kinase B signal transduction
A0070936biological_processprotein K48-linked ubiquitination
A1900076biological_processregulation of cellular response to insulin stimulus
A1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
B0000209biological_processprotein polyubiquitination
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0006006biological_processglucose metabolic process
B0006629biological_processlipid metabolic process
B0010467biological_processgene expression
B0016567biological_processprotein ubiquitination
B0031463cellular_componentCul3-RING ubiquitin ligase complex
B0032868biological_processresponse to insulin
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0043491biological_processphosphatidylinositol 3-kinase/protein kinase B signal transduction
B0070936biological_processprotein K48-linked ubiquitination
B1900076biological_processregulation of cellular response to insulin stimulus
B1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
C0000082biological_processG1/S transition of mitotic cell cycle
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0000209biological_processprotein polyubiquitination
C0000278biological_processmitotic cell cycle
C0000902biological_processcell morphogenesis
C0000922cellular_componentspindle pole
C0001701biological_processin utero embryonic development
C0001822biological_processkidney development
C0001831biological_processtrophectodermal cellular morphogenesis
C0004842molecular_functionubiquitin-protein transferase activity
C0005112molecular_functionNotch binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005794cellular_componentGolgi apparatus
C0005813cellular_componentcentrosome
C0005819cellular_componentspindle
C0005827cellular_componentpolar microtubule
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0006357biological_processregulation of transcription by RNA polymerase II
C0006511biological_processubiquitin-dependent protein catabolic process
C0006513biological_processprotein monoubiquitination
C0006888biological_processendoplasmic reticulum to Golgi vesicle-mediated transport
C0006915biological_processapoptotic process
C0006950biological_processresponse to stress
C0006954biological_processinflammatory response
C0007080biological_processmitotic metaphase chromosome alignment
C0007165biological_processsignal transduction
C0007229biological_processintegrin-mediated signaling pathway
C0007369biological_processgastrulation
C0008284biological_processpositive regulation of cell population proliferation
C0010467biological_processgene expression
C0010468biological_processregulation of gene expression
C0016020cellular_componentmembrane
C0016055biological_processWnt signaling pathway
C0016192biological_processvesicle-mediated transport
C0016477biological_processcell migration
C0016567biological_processprotein ubiquitination
C0017145biological_processstem cell division
C0030030biological_processcell projection organization
C0030163biological_processprotein catabolic process
C0030332molecular_functioncyclin binding
C0031145biological_processanaphase-promoting complex-dependent catabolic process
C0031208molecular_functionPOZ domain binding
C0031398biological_processpositive regulation of protein ubiquitination
C0031461cellular_componentcullin-RING ubiquitin ligase complex
C0031463cellular_componentCul3-RING ubiquitin ligase complex
C0031514cellular_componentmotile cilium
C0031625molecular_functionubiquitin protein ligase binding
C0031648biological_processprotein destabilization
C0032467biological_processpositive regulation of cytokinesis
C0032480biological_processnegative regulation of type I interferon production
C0034599biological_processcellular response to oxidative stress
C0035024biological_processnegative regulation of Rho protein signal transduction
C0036126cellular_componentsperm flagellum
C0040016biological_processembryonic cleavage
C0042802molecular_functionidentical protein binding
C0043149biological_processstress fiber assembly
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0044346biological_processfibroblast apoptotic process
C0045842biological_processpositive regulation of mitotic metaphase/anaphase transition
C0048208biological_processCOPII vesicle coating
C0051301biological_processcell division
C0051865biological_processprotein autoubiquitination
C0061630molecular_functionubiquitin protein ligase activity
C0070062cellular_componentextracellular exosome
C0070936biological_processprotein K48-linked ubiquitination
C0071230biological_processcellular response to amino acid stimulus
C0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
C0072576biological_processliver morphogenesis
C0072686cellular_componentmitotic spindle
C0080090biological_processregulation of primary metabolic process
C0097193biological_processintrinsic apoptotic signaling pathway
C0098794cellular_componentpostsynapse
C0098978cellular_componentglutamatergic synapse
C0140252biological_processregulation protein catabolic process at postsynapse
C0160072molecular_functionubiquitin ligase complex scaffold activity
C1900076biological_processregulation of cellular response to insulin stimulus
C1901992biological_processpositive regulation of mitotic cell cycle phase transition
C1904263biological_processpositive regulation of TORC1 signaling
D0000165biological_processMAPK cascade
D0000209biological_processprotein polyubiquitination
D0004842molecular_functionubiquitin-protein transferase activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005813cellular_componentcentrosome
D0005829cellular_componentcytosol
D0006281biological_processDNA repair
D0006283biological_processtranscription-coupled nucleotide-excision repair
D0006511biological_processubiquitin-dependent protein catabolic process
D0006513biological_processprotein monoubiquitination
D0006974biological_processDNA damage response
D0007283biological_processspermatogenesis
D0008270molecular_functionzinc ion binding
D0016567biological_processprotein ubiquitination
D0016740molecular_functiontransferase activity
D0019005cellular_componentSCF ubiquitin ligase complex
D0019788molecular_functionNEDD8 transferase activity
D0030163biological_processprotein catabolic process
D0030891cellular_componentVCB complex
D0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D0031461cellular_componentcullin-RING ubiquitin ligase complex
D0031462cellular_componentCul2-RING ubiquitin ligase complex
D0031463cellular_componentCul3-RING ubiquitin ligase complex
D0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
D0031465cellular_componentCul4B-RING E3 ubiquitin ligase complex
D0031466cellular_componentCul5-RING ubiquitin ligase complex
D0031467cellular_componentCul7-RING ubiquitin ligase complex
D0031625molecular_functionubiquitin protein ligase binding
D0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
D0032480biological_processnegative regulation of type I interferon production
D0034450molecular_functionubiquitin-ubiquitin ligase activity
D0034599biological_processcellular response to oxidative stress
D0034644biological_processcellular response to UV
D0042110biological_processT cell activation
D0042770biological_processsignal transduction in response to DNA damage
D0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
D0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
D0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
D0043687biological_processpost-translational protein modification
D0044314biological_processprotein K27-linked ubiquitination
D0044877molecular_functionprotein-containing complex binding
D0045116biological_processprotein neddylation
D0045732biological_processpositive regulation of protein catabolic process
D0046627biological_processnegative regulation of insulin receptor signaling pathway
D0046872molecular_functionmetal ion binding
D0060090molecular_functionmolecular adaptor activity
D0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
D0061630molecular_functionubiquitin protein ligase activity
D0061663molecular_functionNEDD8 ligase activity
D0062197biological_processcellular response to chemical stress
D0070936biological_processprotein K48-linked ubiquitination
D0071230biological_processcellular response to amino acid stimulus
D0080008cellular_componentCul4-RING E3 ubiquitin ligase complex
D0090090biological_processnegative regulation of canonical Wnt signaling pathway
D0090734cellular_componentsite of DNA damage
D0097602molecular_functioncullin family protein binding
D0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
D0160240biological_processRNA polymerase II transcription initiation surveillance
D0160276biological_processnegative regulation of beige fat cell differentiation
D1900076biological_processregulation of cellular response to insulin stimulus
D1901525biological_processnegative regulation of mitophagy
D1902499biological_processpositive regulation of protein autoubiquitination
D1902883biological_processnegative regulation of response to oxidative stress
D1904263biological_processpositive regulation of TORC1 signaling
E0000165biological_processMAPK cascade
E0000209biological_processprotein polyubiquitination
E0004842molecular_functionubiquitin-protein transferase activity
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005737cellular_componentcytoplasm
E0005813cellular_componentcentrosome
E0005829cellular_componentcytosol
E0006281biological_processDNA repair
E0006283biological_processtranscription-coupled nucleotide-excision repair
E0006511biological_processubiquitin-dependent protein catabolic process
E0006513biological_processprotein monoubiquitination
E0006974biological_processDNA damage response
E0007283biological_processspermatogenesis
E0008270molecular_functionzinc ion binding
E0016567biological_processprotein ubiquitination
E0016740molecular_functiontransferase activity
E0019005cellular_componentSCF ubiquitin ligase complex
E0019788molecular_functionNEDD8 transferase activity
E0030163biological_processprotein catabolic process
E0030891cellular_componentVCB complex
E0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
E0031461cellular_componentcullin-RING ubiquitin ligase complex
E0031462cellular_componentCul2-RING ubiquitin ligase complex
E0031463cellular_componentCul3-RING ubiquitin ligase complex
E0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
E0031465cellular_componentCul4B-RING E3 ubiquitin ligase complex
E0031466cellular_componentCul5-RING ubiquitin ligase complex
E0031467cellular_componentCul7-RING ubiquitin ligase complex
E0031625molecular_functionubiquitin protein ligase binding
E0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
E0032480biological_processnegative regulation of type I interferon production
E0034450molecular_functionubiquitin-ubiquitin ligase activity
E0034599biological_processcellular response to oxidative stress
E0034644biological_processcellular response to UV
E0042110biological_processT cell activation
E0042770biological_processsignal transduction in response to DNA damage
E0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
E0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
E0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
E0043687biological_processpost-translational protein modification
E0044314biological_processprotein K27-linked ubiquitination
E0044877molecular_functionprotein-containing complex binding
E0045116biological_processprotein neddylation
E0045732biological_processpositive regulation of protein catabolic process
E0046627biological_processnegative regulation of insulin receptor signaling pathway
E0046872molecular_functionmetal ion binding
E0060090molecular_functionmolecular adaptor activity
E0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
E0061630molecular_functionubiquitin protein ligase activity
E0061663molecular_functionNEDD8 ligase activity
E0062197biological_processcellular response to chemical stress
E0070936biological_processprotein K48-linked ubiquitination
E0071230biological_processcellular response to amino acid stimulus
E0080008cellular_componentCul4-RING E3 ubiquitin ligase complex
E0090090biological_processnegative regulation of canonical Wnt signaling pathway
E0090734cellular_componentsite of DNA damage
E0097602molecular_functioncullin family protein binding
E0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
E0160240biological_processRNA polymerase II transcription initiation surveillance
E0160276biological_processnegative regulation of beige fat cell differentiation
E1900076biological_processregulation of cellular response to insulin stimulus
E1901525biological_processnegative regulation of mitophagy
E1902499biological_processpositive regulation of protein autoubiquitination
E1902883biological_processnegative regulation of response to oxidative stress
E1904263biological_processpositive regulation of TORC1 signaling
F0000082biological_processG1/S transition of mitotic cell cycle
F0000122biological_processnegative regulation of transcription by RNA polymerase II
F0000209biological_processprotein polyubiquitination
F0000278biological_processmitotic cell cycle
F0000902biological_processcell morphogenesis
F0000922cellular_componentspindle pole
F0001701biological_processin utero embryonic development
F0001822biological_processkidney development
F0001831biological_processtrophectodermal cellular morphogenesis
F0004842molecular_functionubiquitin-protein transferase activity
F0005112molecular_functionNotch binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005737cellular_componentcytoplasm
F0005794cellular_componentGolgi apparatus
F0005813cellular_componentcentrosome
F0005819cellular_componentspindle
F0005827cellular_componentpolar microtubule
F0005829cellular_componentcytosol
F0005886cellular_componentplasma membrane
F0006357biological_processregulation of transcription by RNA polymerase II
F0006511biological_processubiquitin-dependent protein catabolic process
F0006513biological_processprotein monoubiquitination
F0006888biological_processendoplasmic reticulum to Golgi vesicle-mediated transport
F0006915biological_processapoptotic process
F0006950biological_processresponse to stress
F0006954biological_processinflammatory response
F0007080biological_processmitotic metaphase chromosome alignment
F0007165biological_processsignal transduction
F0007229biological_processintegrin-mediated signaling pathway
F0007369biological_processgastrulation
F0008284biological_processpositive regulation of cell population proliferation
F0010467biological_processgene expression
F0010468biological_processregulation of gene expression
F0016020cellular_componentmembrane
F0016055biological_processWnt signaling pathway
F0016192biological_processvesicle-mediated transport
F0016477biological_processcell migration
F0016567biological_processprotein ubiquitination
F0017145biological_processstem cell division
F0030030biological_processcell projection organization
F0030163biological_processprotein catabolic process
F0030332molecular_functioncyclin binding
F0031145biological_processanaphase-promoting complex-dependent catabolic process
F0031208molecular_functionPOZ domain binding
F0031398biological_processpositive regulation of protein ubiquitination
F0031461cellular_componentcullin-RING ubiquitin ligase complex
F0031463cellular_componentCul3-RING ubiquitin ligase complex
F0031514cellular_componentmotile cilium
F0031625molecular_functionubiquitin protein ligase binding
F0031648biological_processprotein destabilization
F0032467biological_processpositive regulation of cytokinesis
F0032480biological_processnegative regulation of type I interferon production
F0034599biological_processcellular response to oxidative stress
F0035024biological_processnegative regulation of Rho protein signal transduction
F0036126cellular_componentsperm flagellum
F0040016biological_processembryonic cleavage
F0042802molecular_functionidentical protein binding
F0043149biological_processstress fiber assembly
F0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
F0044346biological_processfibroblast apoptotic process
F0045842biological_processpositive regulation of mitotic metaphase/anaphase transition
F0048208biological_processCOPII vesicle coating
F0051301biological_processcell division
F0051865biological_processprotein autoubiquitination
F0061630molecular_functionubiquitin protein ligase activity
F0070062cellular_componentextracellular exosome
F0070936biological_processprotein K48-linked ubiquitination
F0071230biological_processcellular response to amino acid stimulus
F0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
F0072576biological_processliver morphogenesis
F0072686cellular_componentmitotic spindle
F0080090biological_processregulation of primary metabolic process
F0097193biological_processintrinsic apoptotic signaling pathway
F0098794cellular_componentpostsynapse
F0098978cellular_componentglutamatergic synapse
F0140252biological_processregulation protein catabolic process at postsynapse
F0160072molecular_functionubiquitin ligase complex scaffold activity
F1900076biological_processregulation of cellular response to insulin stimulus
F1901992biological_processpositive regulation of mitotic cell cycle phase transition
F1904263biological_processpositive regulation of TORC1 signaling
Functional Information from PROSITE/UniProt
site_idPS01256
Number of Residues28
DetailsCULLIN_1 Cullin family signature. IKkrIegLIEReYLaRtpedrkvYtYvA
ChainResidueDetails
CILE741-ALA768

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues90
DetailsZinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues14
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7Z8B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues124
DetailsDomain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues42
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues32
DetailsCompositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"UniProtKB","id":"Q13616","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues134
DetailsDomain: {"description":"BTB","evidences":[{"source":"PROSITE-ProRule","id":"PRU00037","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues192
DetailsDomain: {"description":"BACK","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues96
DetailsRepeat: {"description":"Kelch 2","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues76
DetailsRepeat: {"description":"Kelch 3","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues92
DetailsRepeat: {"description":"Kelch 5","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

244349

PDB entries from 2025-11-05

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