Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help
SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9OMF

Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1)

Functional Information from GO Data
ChainGOidnamespacecontents
A0004719molecular_functionprotein-L-isoaspartate (D-aspartate) O-methyltransferase activity
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
A0016020cellular_componentmembrane
A0016567biological_processprotein ubiquitination
A0031466cellular_componentCul5-RING ubiquitin ligase complex
A1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
B0000082biological_processG1/S transition of mitotic cell cycle
B0004842molecular_functionubiquitin-protein transferase activity
B0005262molecular_functioncalcium channel activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0007165biological_processsignal transduction
B0010498biological_processproteasomal protein catabolic process
B0016477biological_processcell migration
B0016567biological_processprotein ubiquitination
B0019005cellular_componentSCF ubiquitin ligase complex
B0030335biological_processpositive regulation of cell migration
B0030674molecular_functionprotein-macromolecule adaptor activity
B0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
B0031461cellular_componentcullin-RING ubiquitin ligase complex
B0031466cellular_componentCul5-RING ubiquitin ligase complex
B0031625molecular_functionubiquitin protein ligase binding
B0038023molecular_functionsignaling receptor activity
B0038026biological_processreelin-mediated signaling pathway
B0038128biological_processERBB2 signaling pathway
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0051895biological_processnegative regulation of focal adhesion assembly
B0070588biological_processcalcium ion transmembrane transport
B0070979biological_processprotein K11-linked ubiquitination
B0090734cellular_componentsite of DNA damage
B0097193biological_processintrinsic apoptotic signaling pathway
B0120184biological_processnegative regulation of focal adhesion disassembly
B0160072molecular_functionubiquitin ligase complex scaffold activity
B2001222biological_processregulation of neuron migration
C0001837biological_processepithelial to mesenchymal transition
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006511biological_processubiquitin-dependent protein catabolic process
C0008270molecular_functionzinc ion binding
C0008631biological_processintrinsic apoptotic signaling pathway in response to oxidative stress
C0008637biological_processapoptotic mitochondrial changes
C0010498biological_processproteasomal protein catabolic process
C0016567biological_processprotein ubiquitination
C0016740molecular_functiontransferase activity
C0021799biological_processcerebral cortex radially oriented cell migration
C0021942biological_processradial glia guided migration of Purkinje cell
C0030968biological_processendoplasmic reticulum unfolded protein response
C0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C0031466cellular_componentCul5-RING ubiquitin ligase complex
C0035556biological_processintracellular signal transduction
C0038026biological_processreelin-mediated signaling pathway
C0038162biological_processerythropoietin-mediated signaling pathway
C0043066biological_processnegative regulation of apoptotic process
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0045087biological_processinnate immune response
C0045116biological_processprotein neddylation
C0046314biological_processphosphocreatine biosynthetic process
C0046872molecular_functionmetal ion binding
C0051607biological_processdefense response to virus
C0051894biological_processpositive regulation of focal adhesion assembly
C0051895biological_processnegative regulation of focal adhesion assembly
C0060396biological_processgrowth hormone receptor signaling pathway
C0060397biological_processgrowth hormone receptor signaling pathway via JAK-STAT
C0060400biological_processnegative regulation of growth hormone receptor signaling pathway
C0061630molecular_functionubiquitin protein ligase activity
C0061663molecular_functionNEDD8 ligase activity
C0070979biological_processprotein K11-linked ubiquitination
C0097602molecular_functioncullin family protein binding
C0140896biological_processcGAS/STING signaling pathway
C2001222biological_processregulation of neuron migration
D0000151cellular_componentubiquitin ligase complex
D0001222molecular_functiontranscription corepressor binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
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
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
Functional Information from PROSITE/UniProt
site_idPS01256
Number of Residues28
DetailsCULLIN_1 Cullin family signature. IKeqIewLIEHkYIlRdesdintFiYmA
ChainResidueDetails
BILE753-ALA780
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues23
DetailsRegion: {"description":"AdoMet binding motif","evidences":[{"source":"PubMed","id":"35486881","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues10
DetailsRegion: {"description":"BC-box","evidences":[{"source":"PubMed","id":"35486881","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues3
DetailsRegion: {"description":"CUL-box","evidences":[{"source":"PubMed","id":"35486881","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsActive site: {"evidences":[{"source":"UniProtKB","id":"Q27869","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues61
DetailsDomain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"18805092","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33268465","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34518685","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7ONI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"32513959","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6V9I","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

244693

PDB entries from 2025-11-12

PDB statisticsPDBj update infoContact PDBjnumon