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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8WQC

cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1

Functional Information from GO Data
ChainGOidnamespacecontents
A0000151cellular_componentubiquitin ligase complex
A0005123molecular_functiondeath receptor binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005829cellular_componentcytosol
A0006915biological_processapoptotic process
A0016567biological_processprotein ubiquitination
A0031462cellular_componentCul2-RING ubiquitin ligase complex
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0046872molecular_functionmetal ion binding
A0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
A1902041biological_processregulation of extrinsic apoptotic signaling pathway via death domain receptors
A1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
A2000001biological_processregulation of DNA damage checkpoint
B0006511biological_processubiquitin-dependent protein catabolic process
C0000082biological_processG1/S transition of mitotic cell cycle
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0004842molecular_functionubiquitin-protein transferase activity
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005730cellular_componentnucleolus
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006511biological_processubiquitin-dependent protein catabolic process
C0010498biological_processproteasomal protein catabolic process
C0016567biological_processprotein ubiquitination
C0019005cellular_componentSCF ubiquitin ligase complex
C0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C0031461cellular_componentcullin-RING ubiquitin ligase complex
C0031462cellular_componentCul2-RING ubiquitin ligase complex
C0031625molecular_functionubiquitin protein ligase binding
C0031981cellular_componentnuclear lumen
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0072344biological_processrescue of stalled ribosome
C0097193biological_processintrinsic apoptotic signaling pathway
C0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
C0160072molecular_functionubiquitin ligase complex scaffold activity
C0160276biological_processnegative regulation of beige fat cell differentiation
C1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
C2000104biological_processnegative regulation of DNA-templated DNA replication
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0000151cellular_componentubiquitin ligase complex
D0001222molecular_functiontranscription corepressor binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006351biological_processDNA-templated transcription
D0006367biological_processtranscription initiation at RNA polymerase II promoter
D0006368biological_processtranscription elongation by RNA polymerase II
D0016567biological_processprotein ubiquitination
D0030891cellular_componentVCB complex
D0031462cellular_componentCul2-RING ubiquitin ligase complex
D0031466cellular_componentCul5-RING ubiquitin ligase complex
D0031625molecular_functionubiquitin protein ligase binding
D0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
D0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
D0065003biological_processprotein-containing complex assembly
D0070449cellular_componentelongin complex
D0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
D0140958biological_processtarget-directed miRNA degradation
D1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
D2000104biological_processnegative regulation of DNA-templated DNA replication
E0000082biological_processG1/S transition of mitotic cell cycle
E0000122biological_processnegative regulation of transcription by RNA polymerase II
E0004842molecular_functionubiquitin-protein transferase activity
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005730cellular_componentnucleolus
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006511biological_processubiquitin-dependent protein catabolic process
E0010498biological_processproteasomal protein catabolic process
E0016567biological_processprotein ubiquitination
E0019005cellular_componentSCF ubiquitin ligase complex
E0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
E0031461cellular_componentcullin-RING ubiquitin ligase complex
E0031462cellular_componentCul2-RING ubiquitin ligase complex
E0031625molecular_functionubiquitin protein ligase binding
E0031981cellular_componentnuclear lumen
E0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
E0072344biological_processrescue of stalled ribosome
E0097193biological_processintrinsic apoptotic signaling pathway
E0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
E0160072molecular_functionubiquitin ligase complex scaffold activity
E0160276biological_processnegative regulation of beige fat cell differentiation
E1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
E2000104biological_processnegative regulation of DNA-templated DNA replication
F0008270molecular_functionzinc ion binding
G0000151cellular_componentubiquitin ligase complex
G0005123molecular_functiondeath receptor binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005654cellular_componentnucleoplasm
G0005737cellular_componentcytoplasm
G0005739cellular_componentmitochondrion
G0005829cellular_componentcytosol
G0006915biological_processapoptotic process
G0016567biological_processprotein ubiquitination
G0031462cellular_componentCul2-RING ubiquitin ligase complex
G0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
G0046872molecular_functionmetal ion binding
G0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
G1902041biological_processregulation of extrinsic apoptotic signaling pathway via death domain receptors
G1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
G2000001biological_processregulation of DNA damage checkpoint
H0006511biological_processubiquitin-dependent protein catabolic process
I0000122biological_processnegative regulation of transcription by RNA polymerase II
I0000151cellular_componentubiquitin ligase complex
I0001222molecular_functiontranscription corepressor binding
I0005515molecular_functionprotein binding
I0005634cellular_componentnucleus
I0005654cellular_componentnucleoplasm
I0005737cellular_componentcytoplasm
I0005829cellular_componentcytosol
I0006351biological_processDNA-templated transcription
I0006367biological_processtranscription initiation at RNA polymerase II promoter
I0006368biological_processtranscription elongation by RNA polymerase II
I0016567biological_processprotein ubiquitination
I0030891cellular_componentVCB complex
I0031462cellular_componentCul2-RING ubiquitin ligase complex
I0031466cellular_componentCul5-RING ubiquitin ligase complex
I0031625molecular_functionubiquitin protein ligase binding
I0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
I0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
I0065003biological_processprotein-containing complex assembly
I0070449cellular_componentelongin complex
I0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
I0140958biological_processtarget-directed miRNA degradation
I1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
I2000104biological_processnegative regulation of DNA-templated DNA replication
J0008270molecular_functionzinc ion binding
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0005654cellular_componentnucleoplasm
K0005737cellular_componentcytoplasm
K0005829cellular_componentcytosol
K0006508biological_processproteolysis
K0006511biological_processubiquitin-dependent protein catabolic process
K0009653biological_processanatomical structure morphogenesis
K0016567biological_processprotein ubiquitination
K0019941biological_processmodification-dependent protein catabolic process
K0030162biological_processregulation of proteolysis
K0031386molecular_functionprotein tag activity
K0031625molecular_functionubiquitin protein ligase binding
K0036211biological_processprotein modification process
K0045116biological_processprotein neddylation
K0070062cellular_componentextracellular exosome
K0072757biological_processcellular response to camptothecin
K0098794cellular_componentpostsynapse
K0098978cellular_componentglutamatergic synapse
K0150052biological_processregulation of postsynapse assembly
N0005515molecular_functionprotein binding
N0005634cellular_componentnucleus
N0005654cellular_componentnucleoplasm
N0005737cellular_componentcytoplasm
N0005829cellular_componentcytosol
N0006508biological_processproteolysis
N0006511biological_processubiquitin-dependent protein catabolic process
N0009653biological_processanatomical structure morphogenesis
N0016567biological_processprotein ubiquitination
N0019941biological_processmodification-dependent protein catabolic process
N0030162biological_processregulation of proteolysis
N0031386molecular_functionprotein tag activity
N0031625molecular_functionubiquitin protein ligase binding
N0036211biological_processprotein modification process
N0045116biological_processprotein neddylation
N0070062cellular_componentextracellular exosome
N0072757biological_processcellular response to camptothecin
N0098794cellular_componentpostsynapse
N0098978cellular_componentglutamatergic synapse
N0150052biological_processregulation of postsynapse assembly
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD
ChainResidueDetails
NLYS27-ASP52
site_idPS01256
Number of Residues28
DetailsCULLIN_1 Cullin family signature. IKkcIevLIDKqYIeRsqasadeYsYvA
ChainResidueDetails
CILE718-ALA745
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 Residues120
DetailsDomain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"10092517","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10597293","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
DetailsRegion: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsSite: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues58
DetailsRepeat: {"description":"ANK 1"}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues58
DetailsRepeat: {"description":"ANK 2"}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues58
DetailsRepeat: {"description":"ANK 3"}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues58
DetailsRepeat: {"description":"ANK 4"}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues58
DetailsRepeat: {"description":"ANK 5"}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues60
DetailsRepeat: {"description":"ANK 6"}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues66
DetailsRepeat: {"description":"TPR"}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues88
DetailsRepeat: {"description":"ANK 7"}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues74
DetailsRepeat: {"description":"ANK 8"}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"Q9Z2G0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues2
DetailsSite: {"description":"Cleavage; by a caspase-3-like protease","evidences":[{"source":"PubMed","id":"10542291","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

247947

PDB entries from 2026-01-21

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