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- PDB-9imz: CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to re... -

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Basic information

Entry
Database: PDB / ID: 9imz
TitleCODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate histone supply
Components
  • Codanin-1
  • Histone chaperone ASF1A
KeywordsREPLICATION / Histone chaperone / DNA replication / complex
Function / homology
Function and homology information


histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / osteoblast differentiation / site of double-strand break / nucleosome assembly / histone binding ...histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / osteoblast differentiation / site of double-strand break / nucleosome assembly / histone binding / DNA repair / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone
Similarity search - Domain/homology
Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsJeong, T.K. / Frater, R.C.M. / Yoon, J. / Groth, A. / Song, J.J.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00333346 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00266300 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00440614 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00440614 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply.
Authors: Tae-Kyeong Jeong / R Ciaran MacKenzie Frater / Jongha Yoon / Anja Groth / Ji-Joon Song /
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 ...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.
History
DepositionJul 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)330,9445
Polymers330,9445
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Codanin-1


Mass: 135938.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GenBank AAH66640.1; L1228-Q1241 are EXPRESSION TAG / Source: (gene. exp.) Homo sapiens (human) / Gene: CDAN1, UNQ664/PRO1295 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Protein Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1 / hAsf1a / CCG1-interacting factor A / CIA / hCIA


Mass: 19688.793 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: Escherichia coli BL21(DE3) (bacteria) / 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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1CODANIN-1_ASF1A complexCOMPLEXASF1A is a truncated form (1-172 a.a.)all0RECOMBINANT
2CODANIN-1COMPLEXCODANIN-1 chain A#11RECOMBINANT
3ASF1ACOMPLEXA truncated ASF1A (1-172 a.a.)#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.3 MDaNO
220.135 MDaYES
430.019 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
53Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
32Spodoptera frugiperda (fall armyworm)7108Sf9
53Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1500 mMsodium chlorideNaCl1
220 mMHEPESC8H18N2O4S1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Glow discharge at 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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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 magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4282
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 18 eV

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.4particle selection
4CTFFINDCTFFIND4 4.1.10.CTF correction
7Coot0.9.8.1model fitting
9Coot0.9.8.1model refinement
10PHENIX1.20.1-4487model refinement
11ISOLDE1.3model refinement
14cryoSPARC4.2.1classification
15cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1592795
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56039 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 107.1 / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeInitial refinement model-IDPdb chain residue rangeSource nameTypeDetails
12IO5

2io5

A2IO5A1-15411-154PDBexperimental model
2246-262AlphaFoldin silico modelHMH-N (246-262 a.a) domain of CODANIN-1

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