9CVC | pdb_00009cvc

CDAN1 dimer with three ASF1A

  • Classification: PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-07-29 Released: 2025-03-26 
  • Deposition Author(s): Sedor, S.F., Shao, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), David and Lucile Packard Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of ASF1 engagement by CDAN1.

Sedor, S.F.Shao, S.

(2025) Nat Commun 16: 2599-2599

  • DOI: https://doi.org/10.1038/s41467-025-57950-z
  • Primary Citation of Related Structures:  
    9CVC

  • PubMed Abstract: 

    Codanin-1 (CDAN1) is an essential and ubiquitous protein named after congenital dyserythropoietic anemia type I, an autosomal recessive disease that manifests from mutations in CDAN1 or CDIN1 (CDAN1 interacting nuclease 1). CDAN1 interacts with CDIN1 and the paralogous histone H3-H4 chaperones ASF1A (Anti-Silencing Function 1 A) and ASF1B. However, CDAN1 function remains unclear. Here, we analyze CDAN1 complexes using biochemistry, single-particle cryo-EM, and structural predictions. We find that CDAN1 dimerizes and assembles into cytosolic complexes with CDIN1 and multiple copies of ASF1A/B. One CDAN1 can engage two ASF1 through two B-domains commonly found in ASF1 binding partners and two helices that mimic histone H3 binding. We additionally show that ASF1A and ASF1B have different requirements for CDAN1 engagement. Our findings explain how CDAN1 sequesters ASF1A/B by occupying all functional binding sites known to facilitate histone chaperoning and provide molecular-level insights into this enigmatic complex.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Codanin-1
A, B
1,277Homo sapiensMutation(s): 0 
Gene Names: CDAN1UNQ664/PRO1295
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWY9 (Homo sapiens)
Explore Q8IWY9 
Go to UniProtKB:  Q8IWY9
PHAROS:  Q8IWY9
GTEx:  ENSG00000140326 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IWY9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone chaperone ASF1A
C, D, E
241Homo sapiensMutation(s): 0 
Gene Names: ASF1ACGI-98HSPC146
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y294 (Homo sapiens)
Explore Q9Y294 
Go to UniProtKB:  Q9Y294
PHAROS:  Q9Y294
GTEx:  ENSG00000111875 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y294
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesDP2GM137415
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF31HL157976
David and Lucile Packard FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references