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- EMDB-45959: CDAN1 dimer with three ASF1A -

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Basic information

Entry
Database: EMDB / ID: EMD-45959
TitleCDAN1 dimer with three ASF1A
Map datasharpened map
Sample
  • Complex: CDAN1 bound to ASF1A
    • Protein or peptide: Codanin-1
    • Protein or peptide: Histone chaperone ASF1A
Keywordscytosolic / MIF4G / histone chaperone / PROTEIN BINDING
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSedor SF / Shao S
Funding support United States, 3 items
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, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45959.png

Downloads & links

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Map

FileDownload / File: emd_45959.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.46309817 - 0.6773878
Average (Standard dev.)-0.00063498743 (±0.013575906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_45959_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_45959_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_45959_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CDAN1 bound to ASF1A

EntireName: CDAN1 bound to ASF1A
Components
  • Complex: CDAN1 bound to ASF1A
    • Protein or peptide: Codanin-1
    • Protein or peptide: Histone chaperone ASF1A

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Supramolecule #1: CDAN1 bound to ASF1A

SupramoleculeName: CDAN1 bound to ASF1A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 430 KDa

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Macromolecule #1: Codanin-1

MacromoleculeName: Codanin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.934047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGAWSHPQFE KGSWSHPQFE KGPAGSENLY FQGSGIRDRT MAAVLESLLR EEVSVAAVVR WIARSTQGSE DNAGEAAAL SSLRALRKEF VPFLLNFLRE QSSRVLPQGP PTPAKTPGAS AALPGRPGGP PRGSRGARSQ LFPPTEAQST A AEAPLARR ...String:
MASWSHPQFE KGAWSHPQFE KGSWSHPQFE KGPAGSENLY FQGSGIRDRT MAAVLESLLR EEVSVAAVVR WIARSTQGSE DNAGEAAAL SSLRALRKEF VPFLLNFLRE QSSRVLPQGP PTPAKTPGAS AALPGRPGGP PRGSRGARSQ LFPPTEAQST A AEAPLARR GGRRRGPGPA RERGGRGLEE GVSGESLPGA GGRRLRGSGS PSRPSLTLSD PPNLSNLEEF PPVGSVPPGP TG TKPSRRI NPTPVSEERS LSKPKTCFTS PPISCVPSSQ PSALDTSPWG LGLPPGCRSL QEEREMLRKE RSKQLQQSPT PTC PTPELG SPLPSRTGSL TDEPADPARV SSRQRLELVA LVYSSCIAEN LVPNLFLELF FVFQLLTARR MVTAKDSDPE LSPA VLDSL ESPLFQSIHD CVFFAVQVLE CHFQVLSNLD KGTLKLLAEN ERLLCFSPAL QGRLRAAYEG SVAVVSLVMP PSTQA VSFQ PETDNRANFS SDRAFHTFKK QRDVFYEVLR EWEDHHEEPG WDFEKGLGSR IRAMMGQLSA ACSHSHFVRL FQKQLL QMC QSPGGAGGTV LGEAPDVLSM LGADKLGRLW RLQERLMAPQ SSGGPCPPPT FPGCQGFFRD FILSASSFQF NQHLMDS LS LKIQELNGLA LPQHEPNDED GESDVDWQGE RKQFAVVLLS LRLLAKFLGF VAFLPYRGPE PPPTGELQDS ILALRSQV P PVLDVRTLLQ RGLQARRAVL TVPWLVEFLS FADHVVPLLE YYRDIFTLLL RLHRSLVLSQ ESEGKMCFLN KLLLLAVLG WLFQIPTVPE DLFFLEEGPS YAFEVDTVAP EHGLDNAPVV DQQLLYTCCP YIGELRKLLA SWVSGSSGRS GGFMRKITPT TTTSLGAQP SQTSQGLQAQ LAQAFFHNQP PSLRRTVEFV AERIGSNCVK HIKATLVADL VRQAESLLQE QLVTQGEEGG D PAQLLEIL CSQLCPHGAQ ALALGREFCQ RKSPGAVRAL LPEETPAAVL SSAENIAVGL ATEKACAWLS ANITALIRRE VK AAVSRTL RAQGPEPAAR GERRGCSRAC EHHAPLPSHL ISEIKDVLSL AVGPRDPDEG VSPEHLEQLL GQLGQTLRCR QFL CPPAEQ HLAKCSVELA SLLVADQIPI LGPPAQYRLE RGQARRLLHM LLSLWKEDFQ GPVPLQLLLS PRNVGLLADT RPRE WDLLL FLLRELVEKG LMGRMEIEAC LGSLHQAQWP GDFAEELATL SNLFLAEPHL PEPQLRACEL VQPNRGTVLA QS

UniProtKB: Codanin-1

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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: 27.051857 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVYPYDVPD YAGYPYDVPD YAGSYPYDVP DYAPAGSMAK VQVNNVVVLD NPSPFYNPFQ FEITFECIED LSEDLEWKII YVGSAESEE YDQVLDSVLV GPVPAGRHMF VFQADAPNPG LIPDADAVGV TVVLITCTYR GQEFIRVGYY VNNEYTETEL R ENPPVKPD ...String:
MAVYPYDVPD YAGYPYDVPD YAGSYPYDVP DYAPAGSMAK VQVNNVVVLD NPSPFYNPFQ FEITFECIED LSEDLEWKII YVGSAESEE YDQVLDSVLV GPVPAGRHMF VFQADAPNPG LIPDADAVGV TVVLITCTYR GQEFIRVGYY VNNEYTETEL R ENPPVKPD FSKLQRNILA SNPRVTRFHI NWEDNTEKLE DAESSNPNLQ SLLSTDALPS ASKGWSTSEN SLNVMLESHM DC M

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25056
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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