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- EMDB-60697: CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to re... -

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Basic information

Entry
Database: EMDB / ID: EMD-60697
TitleCODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate histone supply
Map dataEM density map for Codanin-1-Asf1a complex
Sample
  • Complex: CODANIN-1_ASF1A complex
    • Complex: CODANIN-1
      • Protein or peptide: Codanin-1
    • Complex: ASF1A
      • Protein or peptide: Histone chaperone ASF1A
KeywordsHistone chaperone / DNA replication / complex / REPLICATION
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 / nucleosome assembly / site of double-strand break / 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 / nucleosome assembly / site of double-strand break / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsJeong TK / Frater RCM / Yoon J / Groth A / Song JJ
Funding support Korea, Republic Of, 4 items
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, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60697.png

Downloads & links

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Map

FileDownload / File: emd_60697.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map for Codanin-1-Asf1a complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.999761 - 2.9323442
Average (Standard dev.)-0.0003698243 (±0.07472723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60697_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_60697_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_60697_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CODANIN-1_ASF1A complex

EntireName: CODANIN-1_ASF1A complex
Components
  • Complex: CODANIN-1_ASF1A complex
    • Complex: CODANIN-1
      • Protein or peptide: Codanin-1
    • Complex: ASF1A
      • Protein or peptide: Histone chaperone ASF1A

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Supramolecule #1: CODANIN-1_ASF1A complex

SupramoleculeName: CODANIN-1_ASF1A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ASF1A is a truncated form (1-172 a.a.)
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: CODANIN-1

SupramoleculeName: CODANIN-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: CODANIN-1 chain A
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135 KDa

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Supramolecule #3: ASF1A

SupramoleculeName: ASF1A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: A truncated ASF1A (1-172 a.a.)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19 KDa

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Macromolecule #1: Codanin-1

MacromoleculeName: Codanin-1 / type: protein_or_peptide / ID: 1 / Details: GenBank AAH66640.1; L1228-Q1241 are EXPRESSION TAG / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.938969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAVLESLLR EEVSVAAVVR WIARSTQGSE DNAGEAAALS SLRALRKEFV PFLLNFLREQ SSRVLPQGPP TPAKTPGASA ALPGRPGGP PRGSRGARSQ LFPPTEAQST AAEAPLARRG GRRRGPGPAR ERGGRGLEEG VSGESLPGAG GRRLRGSGSP S RPSLTLSD ...String:
MAAVLESLLR EEVSVAAVVR WIARSTQGSE DNAGEAAALS SLRALRKEFV PFLLNFLREQ SSRVLPQGPP TPAKTPGASA ALPGRPGGP PRGSRGARSQ LFPPTEAQST AAEAPLARRG GRRRGPGPAR ERGGRGLEEG VSGESLPGAG GRRLRGSGSP S RPSLTLSD PPNLSNLEEF PPVGSVPPGP TGTKPSRRIN PTPVSEERSL SKPKTCFTSP PISCVPSSQP SALDTSPWGL GL PPGCRSL QEEREMLRKE RSKQLQQSPT PTCPTPELGS PLPSRTGSLT DEPADPARVS SRQRLELVAL VYSSCIAENL VPN LFLELF FVFQLLTARR MVTAKDSDPE LSPAVLDSLE SPLFQSIHDC VFFAVQVLEC HFQVLSNLDK GTLKLLAENE RLLC FSPAL QGRLRAAYEG SVAKVFLVMP PSTQAVSFQP ETDNRANFSS DRAFHTFKKQ RDVFYEVLRE WEDHHEEPGW DFEKG LGSR IRAMMGQLSA ACSHSHFVRL FQKQLLQMCQ SPGGAGGTVL GEAPDVLSML GADKLGRLWR LQERLMAPQS SGGPCP PPT FPGCQGFFRD FILSASSFQF NQHLMDSLSL KIQELNGLAL PQHEPNDEDG ESDVDWQGER KQFAVVLLSL RLLAKFL GF VAFLPYRGPE PPPTGELQDS ILALRSQVPP VLDVRTLLQR GLQARRAVLT VPWLVEFLSF ADHVVPLLEY YRDIFTLL L RLHRSLVLSQ ESEGKMCFLN KLLLLAVLGW LFQIPTVPED LFFLEEGPSY AFEVDTVAPE HGLDNAPVVD QQLLYTCCP YIGELRKLLA SWVSGSSGRS GGFMRKITPT TTTSLGAQPS QTSQGLQAQL AQAFFHNQPP SLRRTVEFVA ERIGSNCVKH IKATLVADL VRQAESLLQE QLVTQGEEGG DPAQLLEILC SQLCPHGAQA LALGREFCQR KSPGAVRALL PEETPAAVLS S AENIAVGL ATEKACAWLS ANITALIRRE VKAAVSRTLR AQGPEPAARG ERRGCSRACE HHAPLPSHLI SEIKDVLSLA VG PRDPDEG VSPEHLEQLL GQLGQTLRCR QFLCPPAEQH LAKCSVELAS LLVADQIPIL GPPAQYRLER GQARRLLHML LSL WKEDFQ GPVPLQLLLS PRNVGLLADT RPREWDLLLF LLRELVEKGL MGRMEIEACL GSLHQAQWPG DFAEELATLS NLFL AEPHL PEPQLRACEL VQPNRGTVLA QSLEACGTKL ENLYFQ

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Macromolecule #2: Histone chaperone ASF1A

MacromoleculeName: Histone chaperone ASF1A / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.688793 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMAKVQVNN VVVLDNPSPF YNPFQFEITF ECIEDLSEDL EWKIIYVGSA ESEEYDQVLD SVLVGPVPAG RHMFVFQADA PNPGLIPDA DAVGVTVVLI TCTYRGQEFI RVGYYVNNEY TETELRENPP VKPDFSKLQR NILASNPRVT RFHINWEDNT E KLEDAESS NPNLQS

UniProtKB: Histone chaperone ASF1A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: Glow discharge at 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 18 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4282 / Average electron dose: 58.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1592795
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2io5


Details: We used 2IO5 for ASF1A startup model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 56039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 37300 / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

2io5

chain_id: A, residue_range: 1-154, source_name: PDB, initial_model_type: experimental model
residue_range: 246-262, source_name: AlphaFold, initial_model_type: in silico modelHMH-N (246-262 a.a) domain of CODANIN-1
RefinementSpace: REAL / Overall B value: 107.1
Output model

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

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