9IMZ | pdb_00009imz

CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate histone supply


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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Literature

CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply.

Jeong, T.K.Frater, R.C.M.Yoon, J.Groth, A.Song, J.J.

(2025) Nat Commun 16: 2181-2181

  • DOI: https://doi.org/10.1038/s41467-025-56976-7
  • Primary Citation of Related Structures:  
    9IMZ

  • PubMed Abstract: 

    ASF1 is a major histone chaperone that regulates the supply of histone H3-H4 and facilitates nucleosome assembly to maintain chromatin structure during DNA replication and transcription. CODANIN-1 negatively regulates the function of ASF1. However, the molecular mechanism by which CODANIN-1 inhibits the ASF1-mediated histone supply remains elusive. Here, we present the cryo-EM structure of a human CODANIN-1_ASF1A complex at 3.75 Å resolution. The structure reveals that CODANIN-1 forms a dimer where each monomer holds two ASF1 molecules, utilizing two B-domains and two histone H3 mimic helices (HMHs). The interaction of CODANIN-1 with ASF1 via the HMH and B-domains inhibits the formation of an ASF1/H3-H4 complex and sequesters ASF1 in the cytoplasm. Our study provides a structural and molecular basis for the function of CODANIN-1 as negative regulator that highjacks ASF1 interaction sites with histones and downstream chaperones to inhibit nucleosome assembly.


  • Organizational Affiliation

    Department of Biological Sciences, KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Codanin-1
A, B
1,241Homo sapiensMutation(s): 0 
Gene Names: CDAN1UNQ664/PRO1295
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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
174Homo 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.8.1
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTISOLDE1.3
RECONSTRUCTIONcryoSPARC4.2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2024-00333346
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00266300
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2024-00440614
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2024-00440614

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release