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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

7B5N

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.

Functional Information from GO Data
ChainGOidnamespacecontents
C0000082biological_processG1/S transition of mitotic cell cycle
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0006355biological_processregulation of DNA-templated transcription
C0006511biological_processubiquitin-dependent protein catabolic process
C0006879biological_processintracellular iron ion homeostasis
C0007346biological_processregulation of mitotic cell cycle
C0010564biological_processregulation of cell cycle process
C0010824biological_processregulation of centrosome duplication
C0014033biological_processneural crest cell differentiation
C0016567biological_processprotein ubiquitination
C0019005cellular_componentSCF ubiquitin ligase complex
C0030510biological_processregulation of BMP signaling pathway
C0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C0031461cellular_componentcullin-RING ubiquitin ligase complex
C0031625molecular_functionubiquitin protein ligase binding
C0032006biological_processregulation of TOR signaling
C0034599biological_processcellular response to oxidative stress
C0042752biological_processregulation of circadian rhythm
C0042981biological_processregulation of apoptotic process
C0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0050727biological_processregulation of inflammatory response
C0051298biological_processcentrosome duplication
C0051726biological_processregulation of cell cycle
C0060173biological_processlimb development
C0060271biological_processcilium assembly
C0070936biological_processprotein K48-linked ubiquitination
C0097193biological_processintrinsic apoptotic signaling pathway
C0160072molecular_functionubiquitin ligase complex scaffold activity
C1901524biological_processregulation of mitophagy
C1904415biological_processregulation of xenophagy
C1990452cellular_componentParkin-FBXW7-Cul1 ubiquitin ligase complex
C2000001biological_processregulation of DNA damage checkpoint
D0000151cellular_componentubiquitin ligase complex
D0000166molecular_functionnucleotide binding
D0000209biological_processprotein polyubiquitination
D0003713molecular_functiontranscription coactivator activity
D0003723molecular_functionRNA binding
D0004842molecular_functionubiquitin-protein transferase activity
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006351biological_processDNA-templated transcription
D0006355biological_processregulation of DNA-templated transcription
D0006511biological_processubiquitin-dependent protein catabolic process
D0008283biological_processcell population proliferation
D0016567biological_processprotein ubiquitination
D0016740molecular_functiontransferase activity
D0019787molecular_functionubiquitin-like protein transferase activity
D0019899molecular_functionenzyme binding
D0031398biological_processpositive regulation of protein ubiquitination
D0031625molecular_functionubiquitin protein ligase binding
D0032446biological_processprotein modification by small protein conjugation
D0036211biological_processprotein modification process
D0044770biological_processcell cycle phase transition
D0045893biological_processpositive regulation of DNA-templated transcription
D0061631molecular_functionubiquitin conjugating enzyme activity
D0070979biological_processprotein K11-linked ubiquitination
D0071383biological_processcellular response to steroid hormone stimulus
D0071385biological_processcellular response to glucocorticoid stimulus
D0097027molecular_functionubiquitin-protein transferase activator activity
D1903955biological_processpositive regulation of protein targeting to mitochondrion
H0000151cellular_componentubiquitin ligase complex
H0004842molecular_functionubiquitin-protein transferase activity
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0006511biological_processubiquitin-dependent protein catabolic process
H0008270molecular_functionzinc ion binding
H0015030cellular_componentCajal body
H0016567biological_processprotein ubiquitination
H0016604cellular_componentnuclear body
H0016740molecular_functiontransferase activity
H0019005cellular_componentSCF ubiquitin ligase complex
H0019787molecular_functionubiquitin-like protein transferase activity
H0031462cellular_componentCul2-RING ubiquitin ligase complex
H0031463cellular_componentCul3-RING ubiquitin ligase complex
H0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
H0031624molecular_functionubiquitin conjugating enzyme binding
H0031625molecular_functionubiquitin protein ligase binding
H0039585biological_processPKR/eIFalpha signaling
H0046872molecular_functionmetal ion binding
H0061630molecular_functionubiquitin protein ligase activity
H0097413cellular_componentLewy body
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
R0000082biological_processG1/S transition of mitotic cell cycle
R0000122biological_processnegative regulation of transcription by RNA polymerase II
R0000165biological_processMAPK cascade
R0000209biological_processprotein polyubiquitination
R0004842molecular_functionubiquitin-protein transferase activity
R0005515molecular_functionprotein binding
R0005634cellular_componentnucleus
R0005654cellular_componentnucleoplasm
R0005737cellular_componentcytoplasm
R0005794cellular_componentGolgi apparatus
R0005813cellular_componentcentrosome
R0005829cellular_componentcytosol
R0006281biological_processDNA repair
R0006283biological_processtranscription-coupled nucleotide-excision repair
R0006289biological_processnucleotide-excision repair
R0006355biological_processregulation of DNA-templated transcription
R0006511biological_processubiquitin-dependent protein catabolic process
R0006513biological_processprotein monoubiquitination
R0006879biological_processintracellular iron ion homeostasis
R0006974biological_processDNA damage response
R0007283biological_processspermatogenesis
R0007346biological_processregulation of mitotic cell cycle
R0008270molecular_functionzinc ion binding
R0008283biological_processcell population proliferation
R0010506biological_processregulation of autophagy
R0010564biological_processregulation of cell cycle process
R0010824biological_processregulation of centrosome duplication
R0014033biological_processneural crest cell differentiation
R0016567biological_processprotein ubiquitination
R0016740molecular_functiontransferase activity
R0019005cellular_componentSCF ubiquitin ligase complex
R0019788molecular_functionNEDD8 transferase activity
R0030174biological_processregulation of DNA-templated DNA replication initiation
R0030510biological_processregulation of BMP signaling pathway
R0030891cellular_componentVCB complex
R0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
R0031297biological_processreplication fork processing
R0031461cellular_componentcullin-RING ubiquitin ligase complex
R0031462cellular_componentCul2-RING ubiquitin ligase complex
R0031463cellular_componentCul3-RING ubiquitin ligase complex
R0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
R0031465cellular_componentCul4B-RING E3 ubiquitin ligase complex
R0031466cellular_componentCul5-RING ubiquitin ligase complex
R0031467cellular_componentCul7-RING ubiquitin ligase complex
R0031625molecular_functionubiquitin protein ligase binding
R0032006biological_processregulation of TOR signaling
R0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
R0032480biological_processnegative regulation of type I interferon production
R0032814biological_processregulation of natural killer cell activation
R0034450molecular_functionubiquitin-ubiquitin ligase activity
R0034599biological_processcellular response to oxidative stress
R0034644biological_processcellular response to UV
R0040029biological_processepigenetic regulation of gene expression
R0042110biological_processT cell activation
R0042127biological_processregulation of cell population proliferation
R0042752biological_processregulation of circadian rhythm
R0042770biological_processsignal transduction in response to DNA damage
R0042981biological_processregulation of apoptotic process
R0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
R0043124biological_processnegative regulation of canonical NF-kappaB signal transduction
R0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
R0043687biological_processpost-translational protein modification
R0044314biological_processprotein K27-linked ubiquitination
R0044877molecular_functionprotein-containing complex binding
R0045116biological_processprotein neddylation
R0045732biological_processpositive regulation of protein catabolic process
R0045995biological_processregulation of embryonic development
R0046627biological_processnegative regulation of insulin receptor signaling pathway
R0046872molecular_functionmetal ion binding
R0050727biological_processregulation of inflammatory response
R0051298biological_processcentrosome duplication
R0051726biological_processregulation of cell cycle
R0060090molecular_functionmolecular adaptor activity
R0060173biological_processlimb development
R0060271biological_processcilium assembly
R0060964biological_processregulation of miRNA-mediated gene silencing
R0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
R0061630molecular_functionubiquitin protein ligase activity
R0061663molecular_functionNEDD8 ligase activity
R0062197biological_processcellular response to chemical stress
R0070936biological_processprotein K48-linked ubiquitination
R0071230biological_processcellular response to amino acid stimulus
R0080008cellular_componentCul4-RING E3 ubiquitin ligase complex
R0080135biological_processregulation of cellular response to stress
R0090090biological_processnegative regulation of canonical Wnt signaling pathway
R0090734cellular_componentsite of DNA damage
R0097602molecular_functioncullin family protein binding
R0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
R0160240biological_processRNA polymerase II transcription initiation surveillance
R0160276biological_processnegative regulation of beige fat cell differentiation
R1900076biological_processregulation of cellular response to insulin stimulus
R1901524biological_processregulation of mitophagy
R1901525biological_processnegative regulation of mitophagy
R1901987biological_processregulation of cell cycle phase transition
R1902412biological_processregulation of mitotic cytokinesis
R1902499biological_processpositive regulation of protein autoubiquitination
R1902883biological_processnegative regulation of response to oxidative stress
R1904178biological_processnegative regulation of adipose tissue development
R1904263biological_processpositive regulation of TORC1 signaling
R1904415biological_processregulation of xenophagy
R1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
R2000001biological_processregulation of DNA damage checkpoint
R2000036biological_processregulation of stem cell population maintenance
R2000104biological_processnegative regulation of DNA-templated DNA replication
Functional Information from PROSITE/UniProt
site_idPS00183
Number of Residues16
DetailsUBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNIdek.GqVCLpvI
ChainResidueDetails
DTYR75-ILE90
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD
ChainResidueDetails
NLYS27-ASP52
ULYS27-ASP52
site_idPS01256
Number of Residues28
DetailsCULLIN_1 Cullin family signature. IKkcIdiLIEKeYLeRvdgekdtYsYlA
ChainResidueDetails
CILE749-ALA776
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues60
DetailsDomain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"10597293","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537541","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18805092","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues50
DetailsZinc finger: {"description":"RING-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues61
DetailsZinc finger: {"description":"IBR-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues31
DetailsZinc finger: {"description":"RING-type 2; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues48
DetailsRegion: {"description":"UBA-like","evidences":[{"source":"PubMed","id":"23707686","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsActive site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21532592","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23707686","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues16
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23707686","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4KBL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KC9","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"15236971","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23707686","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24058416","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1WD2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2M9Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KBL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KC9","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23707686","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24058416","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2M9Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KBL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KC9","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9Z1K5","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsRegion: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues2
DetailsSite: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
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_FI15
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues2
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_FI17
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_FI18
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_FI19
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
site_idSWS_FT_FI20
Number of Residues147
DetailsDomain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues1
DetailsActive site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues1
DetailsM-CSA 438
ChainResidueDetails

247536

PDB entries from 2026-01-14

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