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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly.

Baek, K.Krist, D.T.Prabu, J.R.Hill, S.Klugel, M.Neumaier, L.M.von Gronau, S.Kleiger, G.Schulman, B.A.

(2020) Nature 578: 461-466

  • DOI: 10.1038/s41586-020-2000-y
  • Primary Citation of Related Structures:  
    6TTU

  • PubMed Abstract: 
  • Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation 1 , which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8 2-6 . However, how CRLs catalyse ...

    Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation 1 , which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8 2-6 . 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 β-TRCP 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.


    Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany. schulman@biochem.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/WD repeat-containing protein 1AT605Homo sapiensMutation(s): 0 
Gene Names: BTRCBTRCPFBW1AFBXW1A
Find proteins for Q9Y297 (Homo sapiens)
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PHAROS  Q9Y297
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1S163Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
Find proteins for P63208 (Homo sapiens)
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PHAROS  P63208
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-1C776Homo sapiensMutation(s): 0 
Gene Names: CUL1
Find proteins for Q13616 (Homo sapiens)
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PHAROS  Q13616
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8N77Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
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PHAROS  Q15843
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1R108Homo sapiensMutation(s): 1 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
Find proteins for H2QLR9 (Pan troglodytes)
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2D147Homo sapiensMutation(s): 3 
Gene Names: UBE2D2PUBC1UBC4UBC5BUBCH4UBCH5B
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
Find proteins for P62837 (Homo sapiens)
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PHAROS  P62837
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CU76Homo sapiensMutation(s): 0 
Gene Names: UBC
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PHAROS  P0CG48
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLYI30Homo sapiensMutation(s): 0 
Gene Names: NFKBIAIKBAMAD3NFKBI
Find proteins for P25963 (Homo sapiens)
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PHAROS  P25963
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
IL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2020-02-26
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Database references