8VVY | pdb_00008vvy

Human Cullin-1 in complex with CAND2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanisms of CAND2 in regulating SCF ubiquitin ligases.

Wang, K.Li, L.Kenny, S.Gan, D.Reitsma, J.M.Zhou, Y.Das, C.Liu, X.

(2025) Nat Commun 16: 1998-1998

  • DOI: https://doi.org/10.1038/s41467-025-57065-5
  • Primary Citation of Related Structures:  
    8VVY

  • PubMed Abstract: 

    Protein degradation orchestrated by SKP1·CUL1·F-box protein (SCF) ubiquitin ligases is a fundamental process essential for cellular and organismal function. The dynamic assembly of SCFs, facilitated by CAND1, ensures timely ubiquitination of diverse SCF target proteins. As a homolog of CAND1, CAND2 alone has been implicated in various human diseases, yet its functional mechanisms remain elusive. Here, we investigate the role of CAND2 in human cells and its distinct mode of action compared to CAND1. Using an array of quantitative assays, we demonstrate that CAND2 promotes SCF-mediated protein degradation as an F-box protein exchange factor. While CAND2 binds CUL1 with structure and affinity comparable to CAND1, it exhibits lower efficiency in exchanging F-box proteins. Kinetic measurements reveal a significantly higher K M for CAND2-catalyzed SCF disassembly than CAND1, which explains the lower exchange efficiency of CAND2 and is likely due to conformations of the CAND2·SCF exchange intermediate complex being less favorable for F-box protein dissociation. Our study provides mechanistic insights into the biochemical and structural properties of CAND2, as well as its role in regulating cellular dynamics of SCFs, laying a foundation for understanding contributions of CAND2 to healthy and diseased human cells.


  • Organizational Affiliation
    • Department of Biochemistry, Purdue University, West Lafayette, IN, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-1741Homo sapiensMutation(s): 0 
Gene Names: CUL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13616 (Homo sapiens)
Explore Q13616 
Go to UniProtKB:  Q13616
PHAROS:  Q13616
GTEx:  ENSG00000055130 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13616
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-associated NEDD8-dissociated protein 2B [auth C]1,247Homo sapiensMutation(s): 0 
Gene Names: CAND2KIAA0667TIP120B
UniProt & NIH Common Fund Data Resources
Find proteins for O75155 (Homo sapiens)
Explore O75155 
Go to UniProtKB:  O75155
PHAROS:  O75155
GTEx:  ENSG00000144712 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75155
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC3.2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138016

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references