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- PDB-9t4v: Activation intermediate of ALC1/CHD1L bound to a PARylated nucleosome -

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Basic information

Entry
Database: PDB / ID: 9t4v
TitleActivation intermediate of ALC1/CHD1L bound to a PARylated nucleosome
Components
  • (Widom 601 sequence) x 2
  • Chromodomain-helicase-DNA-binding protein 1-like
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / ALC1 / CHD1L / chromatin remodeler / DNA damage response / nucleosome / poly(ADP-ribose)
Function / homology
Function and homology information


poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / histone reader activity / site of DNA damage / nucleosome binding / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin ...poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / histone reader activity / site of DNA damage / nucleosome binding / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / site of double-strand break / chromatin remodeling / protein heterodimerization activity / DNA repair / nucleotide binding / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 1-like / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2A conserved site ...Chromodomain-helicase-DNA-binding protein 1-like / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Macro domain profile. / Macro domain / Macro domain-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Chromodomain-helicase-DNA-binding protein 1-like
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsBridges, H.R. / Bacic, L. / Deindl, S. / Gaullier, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2025
Title: Activation intermediate of ALC1/CHD1L bound to a PARylated nucleosome
Authors: Bridges, H.R. / Bacic, L. / Deindl, S. / Gaullier, G.
History
DepositionNov 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 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: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: Widom 601 sequence
J: Widom 601 sequence
K: Chromodomain-helicase-DNA-binding protein 1-like


Theoretical massNumber of molelcules
Total (without water)306,81411
Polymers306,81411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.2


Mass: 15403.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Chromodomain-helicase-DNA-binding protein 1-like / Amplified in liver cancer protein 1


Mass: 98906.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1L, ALC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WJ1, DNA helicase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain Widom 601 sequence


Mass: 49175.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain Widom 601 sequence


Mass: 49606.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

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: ALC1/CHD1L bound to a PARylated nucleosome / Type: COMPLEX
Details: The nucleosome was PARylated by PARP2 and HPF1 before addition of ALC1.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.305 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.

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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: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 33998 / Details: Total dose was fractionated over 40 movie frames.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2EPU2.6.1image acquisition
4cryoSPARC4.7.1CTF correction
7UCSF ChimeraX1.10.1model fitting
8ISOLDE1.10.1model fitting
10PHENIX1.21.2-5419model refinement
11cryoSPARC4.7.1initial Euler assignment
12cryoSPARC4.7.1final Euler assignment
13cryoSPARC4.7.1classification
14cryoSPARC4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2001174
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15740 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameType
18B0A

8b0a

A8B0AA1PDBexperimental model
28B0A

8b0a

B8B0AB1PDBexperimental model
38B0A

8b0a

C8B0AC1PDBexperimental model
48B0A

8b0a

D8B0AD1PDBexperimental model
58B0A

8b0a

E8B0AE1PDBexperimental model
68B0A

8b0a

F8B0AF1PDBexperimental model
78B0A

8b0a

G8B0AG1PDBexperimental model
88B0A

8b0a

H8B0AH1PDBexperimental model
98B0A

8b0a

I8B0AI1PDBexperimental model
108B0A

8b0a

J8B0AJ1PDBexperimental model
11AF-Q86WJ1-F1-v4K2AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 335.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007919862
ELECTRON MICROSCOPYf_angle_d1.291728072
ELECTRON MICROSCOPYf_chiral_restr0.07223150
ELECTRON MICROSCOPYf_plane_restr0.01612551
ELECTRON MICROSCOPYf_dihedral_angle_d23.02548242

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