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- PDB-9cvc: CDAN1 dimer with three ASF1A -

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Basic information

Entry
Database: PDB / ID: 9cvc
TitleCDAN1 dimer with three ASF1A
Components
  • Codanin-1
  • Histone chaperone ASF1A
KeywordsPROTEIN BINDING / cytosolic / MIF4G / histone chaperone
Function / homology
Function and homology information


histone chaperone activity / import into nucleus / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / endomembrane system / osteoblast differentiation / intracellular protein localization ...histone chaperone activity / import into nucleus / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / endomembrane system / osteoblast differentiation / intracellular protein localization / nucleosome assembly / chromatin organization / site of double-strand break / histone binding / DNA repair / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Codanin-1, C-terminal domain / Codanin-1 / Codanin-1 C-terminus / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone
Similarity search - Domain/homology
Codanin-1 / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSedor, S.F. / Shao, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137415 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F31HL157976 United States
David and Lucile Packard Foundation United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of ASF1 engagement by CDAN1.
Authors: Samantha F Sedor / Sichen Shao /
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 ...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.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Codanin-1
B: Codanin-1
C: Histone chaperone ASF1A
D: Histone chaperone ASF1A
E: Histone chaperone ASF1A


Theoretical massNumber of molelcules
Total (without water)361,0245
Polymers361,0245
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Codanin-1


Mass: 139934.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDAN1, UNQ664/PRO1295 / Production host: Homo sapiens (human) / References: UniProt: Q8IWY9
#2: Protein Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1 / hAsf1a / CCG1-interacting factor A / CIA / hCIA


Mass: 27051.857 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Production host: Homo sapiens (human) / References: UniProt: Q9Y294
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CDAN1 bound to ASF1A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.43 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25056 / Symmetry type: POINT

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