7Z8B | pdb_00007z8b

Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure of CRL7 FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation.

Hopf, L.V.M.Baek, K.Klugel, M.von Gronau, S.Xiong, Y.Schulman, B.A.

(2022) Nat Struct Mol Biol 29: 854-862

  • DOI: https://doi.org/10.1038/s41594-022-00815-6
  • Primary Citation Related Structures: 
    7Z8B

  • PubMed Abstract: 

    Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). However, the vertebrate-specific CRL7 FBXW8 is of interest because it eludes existing models, yet its constituent cullin CUL7 and F-box protein FBXW8 are essential for development, and CUL7 mutations cause 3M syndrome. In this study, cryo-EM and biochemical analyses reveal the CRL7 FBXW8 assembly. CUL7's exclusivity for FBXW8 among all F-box proteins is explained by its unique F-box-independent binding mode. In CRL7 FBXW8 , the RBX1 (also known as ROC1) RING domain is constrained in an orientation incompatible with binding E2~NEDD8 or E2~ubiquitin intermediates. Accordingly, purified recombinant CRL7 FBXW8 lacks auto-neddylation and ubiquitination activities. Instead, our data indicate that CRL7 serves as a substrate receptor linked via SKP1-FBXW8 to a neddylated CUL1-RBX1 catalytic module mediating ubiquitination. The structure reveals a distinctive CRL-CRL partnership, and provides a framework for understanding CUL7 assemblies safeguarding human health.


  • Organizational Affiliation
    • Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 290.36 kDa 
  • Atom Count: 14,463 
  • Modeled Residue Count: 1,896 
  • Deposited Residue Count: 2,571 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cullin-7A [auth C]1,700Homo sapiensMutation(s): 1 
Gene Names: CUL7KIAA0076
UniProt & NIH Common Fund Data Resources
Find proteins for Q14999 (Homo sapiens)
Explore Q14999 
Go to UniProtKB:  Q14999
PHAROS:  Q14999
GTEx:  ENSG00000044090 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14999
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
F-box/WD repeat-containing protein 8B [auth F]600Homo sapiensMutation(s): 0 
Gene Names: FBXW8FBW6FBW8FBX29FBXO29FBXW6
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N3Y1 (Homo sapiens)
Explore Q8N3Y1 
Go to UniProtKB:  Q8N3Y1
PHAROS:  Q8N3Y1
GTEx:  ENSG00000174989 
Entity Groups
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UniProt GroupQ8N3Y1
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1C [auth R]108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens)
Explore P62877 
Go to UniProtKB:  P62877
PHAROS:  P62877
GTEx:  ENSG00000100387 
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UniProt GroupP62877
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1D [auth S]163Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558 
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UniProt GroupP63208
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union789016
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Database references
  • Version 1.3: 2024-07-24
    Changes: Data collection