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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6R7F

Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome

Functional Information from GO Data
ChainGOidnamespacecontents
B0000122biological_processnegative regulation of transcription by RNA polymerase II
B0000338biological_processprotein deneddylation
B0001833biological_processinner cell mass cell proliferation
B0001834biological_processtrophectodermal cell proliferation
B0003714molecular_functiontranscription corepressor activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006366biological_processtranscription by RNA polymerase II
B0006468biological_processprotein phosphorylation
B0007165biological_processsignal transduction
B0008180cellular_componentCOP9 signalosome
B0030182biological_processneuron differentiation
B0032991cellular_componentprotein-containing complex
B0035914biological_processskeletal muscle cell differentiation
B0045116biological_processprotein neddylation
B0045892biological_processnegative regulation of DNA-templated transcription
B2000434biological_processregulation of protein neddylation
C0000338biological_processprotein deneddylation
C0001701biological_processin utero embryonic development
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006511biological_processubiquitin-dependent protein catabolic process
C0007165biological_processsignal transduction
C0008180cellular_componentCOP9 signalosome
C0009416biological_processresponse to light stimulus
C0043516biological_processregulation of DNA damage response, signal transduction by p53 class mediator
C0045116biological_processprotein neddylation
C0048471cellular_componentperinuclear region of cytoplasm
C2000434biological_processregulation of protein neddylation
D0000338biological_processprotein deneddylation
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0008021cellular_componentsynaptic vesicle
D0008180cellular_componentCOP9 signalosome
D0016607cellular_componentnuclear speck
D0019784molecular_functiondeNEDDylase activity
D0030054cellular_componentcell junction
D0031410cellular_componentcytoplasmic vesicle
D0032991cellular_componentprotein-containing complex
D0045116biological_processprotein neddylation
D0045202cellular_componentsynapse
D2000434biological_processregulation of protein neddylation
E0000338biological_processprotein deneddylation
E0000785cellular_componentchromatin
E0003713molecular_functiontranscription coactivator activity
E0003743molecular_functiontranslation initiation factor activity
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0005852cellular_componenteukaryotic translation initiation factor 3 complex
E0006412biological_processtranslation
E0006413biological_processtranslational initiation
E0006508biological_processproteolysis
E0008021cellular_componentsynaptic vesicle
E0008180cellular_componentCOP9 signalosome
E0008233molecular_functionpeptidase activity
E0008237molecular_functionmetallopeptidase activity
E0016787molecular_functionhydrolase activity
E0019784molecular_functiondeNEDDylase activity
E0019899molecular_functionenzyme binding
E0031410cellular_componentcytoplasmic vesicle
E0035718molecular_functionmacrophage migration inhibitory factor binding
E0043066biological_processnegative regulation of apoptotic process
E0043687biological_processpost-translational protein modification
E0045116biological_processprotein neddylation
E0045202cellular_componentsynapse
E0045944biological_processpositive regulation of transcription by RNA polymerase II
E0046328biological_processregulation of JNK cascade
E0046872molecular_functionmetal ion binding
E0048471cellular_componentperinuclear region of cytoplasm
E0051091biological_processpositive regulation of DNA-binding transcription factor activity
E0051726biological_processregulation of cell cycle
E0140492molecular_functionmetal-dependent deubiquitinase activity
E1903894biological_processregulation of IRE1-mediated unfolded protein response
E1990182biological_processexosomal secretion
E2000434biological_processregulation of protein neddylation
F0000338biological_processprotein deneddylation
F0008180cellular_componentCOP9 signalosome
F0008233molecular_functionpeptidase activity
F0008237molecular_functionmetallopeptidase activity
G0008180cellular_componentCOP9 signalosome
G0010387biological_processCOP9 signalosome assembly
H0000338biological_processprotein deneddylation
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0006468biological_processprotein phosphorylation
H0007250biological_processactivation of NF-kappaB-inducing kinase activity
H0008180cellular_componentCOP9 signalosome
H0008285biological_processnegative regulation of cell population proliferation
H0010387biological_processCOP9 signalosome assembly
H0045116biological_processprotein neddylation
H0048471cellular_componentperinuclear region of cytoplasm
H0070062cellular_componentextracellular exosome
H2000434biological_processregulation of protein neddylation
N0005515molecular_functionprotein binding
N0005634cellular_componentnucleus
N0005654cellular_componentnucleoplasm
N0005737cellular_componentcytoplasm
N0005829cellular_componentcytosol
N0006357biological_processregulation of transcription by RNA polymerase II
N0006508biological_processproteolysis
N0006511biological_processubiquitin-dependent protein catabolic process
N0008104biological_processprotein localization
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
O0000082biological_processG1/S transition of mitotic cell cycle
O0004842molecular_functionubiquitin-protein transferase activity
O0005515molecular_functionprotein binding
O0005634cellular_componentnucleus
O0005654cellular_componentnucleoplasm
O0005730cellular_componentnucleolus
O0005829cellular_componentcytosol
O0006511biological_processubiquitin-dependent protein catabolic process
O0010498biological_processproteasomal protein catabolic process
O0016567biological_processprotein ubiquitination
O0019005cellular_componentSCF ubiquitin ligase complex
O0030163biological_processprotein catabolic process
O0030674molecular_functionprotein-macromolecule adaptor activity
O0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
O0031461cellular_componentcullin-RING ubiquitin ligase complex
O0031462cellular_componentCul2-RING ubiquitin ligase complex
O0031625molecular_functionubiquitin protein ligase binding
O0031981cellular_componentnuclear lumen
O0097193biological_processintrinsic apoptotic signaling pathway
O0140627biological_processubiquitin-dependent protein catabolic process via the C-end degron rule pathway
O0160072molecular_functionubiquitin ligase complex scaffold activity
P0000151cellular_componentubiquitin ligase complex
P0001222molecular_functiontranscription corepressor binding
P0005515molecular_functionprotein binding
P0005634cellular_componentnucleus
P0005654cellular_componentnucleoplasm
P0005737cellular_componentcytoplasm
P0005829cellular_componentcytosol
P0006367biological_processtranscription initiation at RNA polymerase II promoter
P0006368biological_processtranscription elongation by RNA polymerase II
P0016567biological_processprotein ubiquitination
P0030891cellular_componentVCB complex
P0031462cellular_componentCul2-RING ubiquitin ligase complex
P0031466cellular_componentCul5-RING ubiquitin ligase complex
P0031625molecular_functionubiquitin protein ligase binding
P0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
P0065003biological_processprotein-containing complex assembly
P0070449cellular_componentelongin complex
P0140958biological_processtarget-directed miRNA degradation
Q0000151cellular_componentubiquitin ligase complex
Q0001222molecular_functiontranscription corepressor binding
Q0005515molecular_functionprotein binding
Q0005634cellular_componentnucleus
Q0005654cellular_componentnucleoplasm
Q0005737cellular_componentcytoplasm
Q0005829cellular_componentcytosol
Q0006357biological_processregulation of transcription by RNA polymerase II
Q0006367biological_processtranscription initiation at RNA polymerase II promoter
Q0006511biological_processubiquitin-dependent protein catabolic process
Q0016567biological_processprotein ubiquitination
Q0030674molecular_functionprotein-macromolecule adaptor activity
Q0031462cellular_componentCul2-RING ubiquitin ligase complex
Q0031466cellular_componentCul5-RING ubiquitin ligase complex
Q0070449cellular_componentelongin complex
Q0140958biological_processtarget-directed miRNA degradation
R0008270molecular_functionzinc ion binding
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
OILE718-ALA745
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues661
DetailsDomain: {"description":"PCI","evidences":[{"source":"PROSITE-ProRule","id":"PRU01185","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18850735","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1
DetailsModified residue: {"description":"N-acetylalanine","evidences":[{"source":"PubMed","id":"18850735","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2005","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Quadroni M."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsModified residue: {"description":"N-acetylalanine","evidences":[{"source":"PubMed","id":"18850735","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues270
DetailsDomain: {"description":"MPN","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues13
DetailsMotif: {"description":"JAMM motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues55
DetailsRegion: {"description":"Involved in binding to CCT complex"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues9
DetailsRegion: {"description":"Interaction with Elongin BC complex"}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues65
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues26
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues11
DetailsCompositional bias: {"description":"Polar residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
DetailsModified residue: {"description":"N-acetylmethionine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2009","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Waridel P.","Quadroni M."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62869","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P62869","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues2
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_FI19
Number of Residues45
DetailsZinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI20
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_FI21
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_FI22
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_FI23
Number of Residues2
DetailsRegion: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues2
DetailsSite: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI25
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_FI26
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI27
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

238582

PDB entries from 2025-07-09

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