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Structure paper

TitleNEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly.
Journal, issue, pagesNature, Vol. 578, Issue 7795, Page 461-466, Year 2020
Publish dateFeb 12, 2020
AuthorsKheewoong Baek / David T Krist / J Rajan Prabu / Spencer Hill / Maren Klügel / Lisa-Marie Neumaier / Susanne von Gronau / Gary Kleiger / Brenda A Schulman /
PubMed AbstractEukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. ...Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. However, how CRLs catalyse ubiquitylation, and the basis of NEDD8 activation, remain unknown. Here we report the cryo-electron microscopy structure of a chemically trapped complex that represents the ubiquitylation intermediate, in which the neddylated CRL1 promotes the transfer of ubiquitin from the E2 ubiquitin-conjugating enzyme UBE2D to its recruited substrate, phosphorylated IκBα. NEDD8 acts as a nexus that binds disparate cullin elements and the RING-activated ubiquitin-linked UBE2D. Local structural remodelling of NEDD8 and large-scale movements of CRL domains converge to juxtapose the substrate and the ubiquitylation active site. These findings explain how a distinctive ubiquitin-like protein alters the functions of its targets, and show how numerous NEDD8-dependent interprotein interactions and conformational changes synergistically configure a catalytic CRL architecture that is both robust, to enable rapid ubiquitylation of the substrate, and fragile, to enable the subsequent functions of cullin-RING proteins.
External linksNature / PubMed:32051583 / PubMed Central
MethodsEM (single particle)
Resolution3.7 - 9.4 Å
Structure data

EMDB-10578:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase: NEDD8-CUL1-RBX1 SKP1-dimeric bTRCP2-IkBa-(UB)~UBE2D2
Method: EM (single particle) / Resolution: 9.3 Å

EMDB-10579:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase: NEDD8-CUL1-RBX1-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D3
Method: EM (single particle) / Resolution: 8.6 Å

EMDB-10580:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D3
Method: EM (single particle) / Resolution: 9.4 Å

EMDB-10581:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
Method: EM (single particle) / Resolution: 8.4 Å

EMDB-10582:
Dynamic Cullin-RING E3 ligase: CUL1-RBX1-SKP1-b-TRCP1dD-IkBa
Method: EM (single particle) / Resolution: 4.64 Å

EMDB-10583:
Dynamic neddylated Cullin-RING E3 ligase: NEDD8-CUL1-RBX1-SKP1-b-TRCP1dD-IkBa
Method: EM (single particle) / Resolution: 6.7 Å

10585

6ttu

EMDB-10585, PDB-6ttu:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
Method: EM (single particle) / Resolution: 3.7 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
  • Pan troglodytes (chimpanzee)
KeywordsLIGASE / Ubiquitin / E3 ligase / NEDD8 / cullin / CUL1 / RBX1 / SKP1 / TRCP / UBE2D / IkBalpha / Neddylation / Ubiquitylation

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