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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

2HYE

Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0000781cellular_componentchromosome, telomeric region
A0003676molecular_functionnucleic acid binding
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0005515molecular_functionprotein binding
A0005615cellular_componentextracellular space
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0006281biological_processDNA repair
A0006289biological_processnucleotide-excision repair
A0006511biological_processubiquitin-dependent protein catabolic process
A0006974biological_processDNA damage response
A0007056biological_processspindle assembly involved in female meiosis
A0007283biological_processspermatogenesis
A0008283biological_processcell population proliferation
A0010498biological_processproteasomal protein catabolic process
A0010506biological_processregulation of autophagy
A0016567biological_processprotein ubiquitination
A0019076biological_processviral release from host cell
A0030174biological_processregulation of DNA-templated DNA replication initiation
A0030674molecular_functionprotein-macromolecule adaptor activity
A0031297biological_processreplication fork processing
A0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
A0031465cellular_componentCul4B-RING E3 ubiquitin ligase complex
A0032814biological_processregulation of natural killer cell activation
A0032991cellular_componentprotein-containing complex
A0034644biological_processcellular response to UV
A0035861cellular_componentsite of double-strand break
A0040029biological_processepigenetic regulation of gene expression
A0042127biological_processregulation of cell population proliferation
A0042752biological_processregulation of circadian rhythm
A0042981biological_processregulation of apoptotic process
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0044725biological_processepigenetic programming in the zygotic pronuclei
A0044877molecular_functionprotein-containing complex binding
A0045070biological_processpositive regulation of viral genome replication
A0045722biological_processpositive regulation of gluconeogenesis
A0045732biological_processpositive regulation of protein catabolic process
A0045995biological_processregulation of embryonic development
A0046726biological_processpositive regulation by virus of viral protein levels in host cell
A0048511biological_processrhythmic process
A0051702biological_processbiological process involved in interaction with symbiont
A0060964biological_processregulation of miRNA-mediated gene silencing
A0070062cellular_componentextracellular exosome
A0070914biological_processUV-damage excision repair
A0071987molecular_functionWD40-repeat domain binding
A0080008cellular_componentCul4-RING E3 ubiquitin ligase complex
A0080135biological_processregulation of cellular response to stress
A0097602molecular_functioncullin family protein binding
A0160072molecular_functionubiquitin ligase complex scaffold activity
A1901987biological_processregulation of cell cycle phase transition
A1901990biological_processregulation of mitotic cell cycle phase transition
A1902412biological_processregulation of mitotic cytokinesis
A1904178biological_processnegative regulation of adipose tissue development
A2000036biological_processregulation of stem cell population maintenance
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0030430cellular_componenthost cell cytoplasm
B0039502biological_processsymbiont-mediated suppression of host type I interferon-mediated signaling pathway
B0039554biological_processsymbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity
B0039563biological_processsymbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity
B0039564biological_processsymbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity
B0046872molecular_functionmetal ion binding
B0052031biological_processsymbiont-mediated perturbation of host defense response
B0052170biological_processsymbiont-mediated suppression of host innate immune response
B0060090molecular_functionmolecular adaptor activity
B1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
C0000082biological_processG1/S transition of mitotic cell cycle
C0001701biological_processin utero embryonic development
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0006281biological_processDNA repair
C0006289biological_processnucleotide-excision repair
C0006511biological_processubiquitin-dependent protein catabolic process
C0006974biological_processDNA damage response
C0007283biological_processspermatogenesis
C0008283biological_processcell population proliferation
C0010506biological_processregulation of autophagy
C0016567biological_processprotein ubiquitination
C0030174biological_processregulation of DNA-templated DNA replication initiation
C0031297biological_processreplication fork processing
C0031461cellular_componentcullin-RING ubiquitin ligase complex
C0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
C0031625molecular_functionubiquitin protein ligase binding
C0032502biological_processdevelopmental process
C0032814biological_processregulation of natural killer cell activation
C0034644biological_processcellular response to UV
C0040029biological_processepigenetic regulation of gene expression
C0042110biological_processT cell activation
C0042127biological_processregulation of cell population proliferation
C0042254biological_processribosome biogenesis
C0042981biological_processregulation of apoptotic process
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0045732biological_processpositive regulation of protein catabolic process
C0045995biological_processregulation of embryonic development
C0048511biological_processrhythmic process
C0051246biological_processregulation of protein metabolic process
C0060964biological_processregulation of miRNA-mediated gene silencing
C0061630molecular_functionubiquitin protein ligase activity
C0080008cellular_componentCul4-RING E3 ubiquitin ligase complex
C0080135biological_processregulation of cellular response to stress
C0097193biological_processintrinsic apoptotic signaling pathway
C0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
C0160072molecular_functionubiquitin ligase complex scaffold activity
C1901987biological_processregulation of cell cycle phase transition
C1902412biological_processregulation of mitotic cytokinesis
C1904178biological_processnegative regulation of adipose tissue development
C2000036biological_processregulation of stem cell population maintenance
D0000082biological_processG1/S transition of mitotic cell cycle
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0000165biological_processMAPK cascade
D0000209biological_processprotein polyubiquitination
D0004842molecular_functionubiquitin-protein transferase activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005794cellular_componentGolgi apparatus
D0005813cellular_componentcentrosome
D0005829cellular_componentcytosol
D0006281biological_processDNA repair
D0006283biological_processtranscription-coupled nucleotide-excision repair
D0006289biological_processnucleotide-excision repair
D0006355biological_processregulation of DNA-templated transcription
D0006511biological_processubiquitin-dependent protein catabolic process
D0006513biological_processprotein monoubiquitination
D0006879biological_processintracellular iron ion homeostasis
D0006974biological_processDNA damage response
D0007283biological_processspermatogenesis
D0007346biological_processregulation of mitotic cell cycle
D0008270molecular_functionzinc ion binding
D0008283biological_processcell population proliferation
D0010506biological_processregulation of autophagy
D0010564biological_processregulation of cell cycle process
D0010824biological_processregulation of centrosome duplication
D0014033biological_processneural crest cell differentiation
D0016567biological_processprotein ubiquitination
D0016740molecular_functiontransferase activity
D0019005cellular_componentSCF ubiquitin ligase complex
D0019788molecular_functionNEDD8 transferase activity
D0030174biological_processregulation of DNA-templated DNA replication initiation
D0030510biological_processregulation of BMP signaling pathway
D0030891cellular_componentVCB complex
D0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D0031297biological_processreplication fork processing
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
D0032006biological_processregulation of TOR signaling
D0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
D0032480biological_processnegative regulation of type I interferon production
D0032814biological_processregulation of natural killer cell activation
D0034450molecular_functionubiquitin-ubiquitin ligase activity
D0034599biological_processcellular response to oxidative stress
D0034644biological_processcellular response to UV
D0040029biological_processepigenetic regulation of gene expression
D0042110biological_processT cell activation
D0042127biological_processregulation of cell population proliferation
D0042752biological_processregulation of circadian rhythm
D0042770biological_processsignal transduction in response to DNA damage
D0042981biological_processregulation of apoptotic process
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
D0045995biological_processregulation of embryonic development
D0046627biological_processnegative regulation of insulin receptor signaling pathway
D0046872molecular_functionmetal ion binding
D0050727biological_processregulation of inflammatory response
D0051298biological_processcentrosome duplication
D0051726biological_processregulation of cell cycle
D0060090molecular_functionmolecular adaptor activity
D0060173biological_processlimb development
D0060271biological_processcilium assembly
D0060964biological_processregulation of miRNA-mediated gene silencing
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
D0080135biological_processregulation of cellular response to stress
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
D1901524biological_processregulation of mitophagy
D1901525biological_processnegative regulation of mitophagy
D1901987biological_processregulation of cell cycle phase transition
D1902412biological_processregulation of mitotic cytokinesis
D1902499biological_processpositive regulation of protein autoubiquitination
D1902883biological_processnegative regulation of response to oxidative stress
D1904178biological_processnegative regulation of adipose tissue development
D1904263biological_processpositive regulation of TORC1 signaling
D1904415biological_processregulation of xenophagy
D1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
D2000001biological_processregulation of DNA damage checkpoint
D2000036biological_processregulation of stem cell population maintenance
D2000104biological_processnegative regulation of DNA-templated DNA replication
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 3001
ChainResidue
BCYS194
BCYS206
BCYS208
BCYS211
site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 3002
ChainResidue
BHIS171
BCYS190
BCYS215
BCYS218
site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 4001
ChainResidue
DCYS45
DHIS80
DCYS83
DCYS42
site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 4003
ChainResidue
DCYS53
DCYS56
DCYS68
DHIS82
site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 4002
ChainResidue
DCYS75
DHIS77
DCYS94
DASP97
Functional Information from PROSITE/UniProt
site_idPS01256
Number of Residues28
DetailsCULLIN_1 Cullin family signature. LKkrIesLIDRdYMeRdkdnpnqYhYvA
ChainResidueDetails
CLEU732-ALA759
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues766
DetailsRegion: {"description":"Interaction with CDT1","evidences":[{"source":"PubMed","id":"15448697","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues343
DetailsRegion: {"description":"WD repeat beta-propeller A"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues316
DetailsRegion: {"description":"WD repeat beta-propeller B; Interaction with CUL4A"}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues334
DetailsRegion: {"description":"WD repeat beta-propeller C"}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues369
DetailsRegion: {"description":"Interaction with CDT1 and CUL4A","evidences":[{"source":"PubMed","id":"15448697","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23328395","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4I1S","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues5
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16413485","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16964240","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23328395","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2B5L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I1S","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16413485","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23328395","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2B5L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I1S","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues60
DetailsDomain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues45
DetailsZinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues7
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_FI17
Number of Residues4
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_FI18
Number of Residues1
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

246704

PDB entries from 2025-12-24

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