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- EMDB-55533: Activation intermediate of ALC1/CHD1L bound to a PARylated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-55533
TitleActivation intermediate of ALC1/CHD1L bound to a PARylated nucleosome
Map dataSharpened map
Sample
  • Complex: ALC1/CHD1L bound to a PARylated nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: Widom 601 sequence
    • DNA: Widom 601 sequence
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1-like
KeywordsALC1 / CHD1L / chromatin remodeler / DNA damage response / nucleosome / poly(ADP-ribose) / DNA BINDING PROTEIN
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 / Dual Incision in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / Dual Incision in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome / heterochromatin formation / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsBridges HR / Bacic L / Deindl S / Gaullier G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2025
Title: Activation intermediate of ALC1/CHD1L bound to a PARylated nucleosome
Authors: Bridges HR / Bacic L / Deindl S / Gaullier G
History
DepositionNov 2, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55533.png

Downloads & links

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Map

FileDownload / File: emd_55533.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 416 pix.
= 349.44 Å		0.84 Å/pix.
x 416 pix.
= 349.44 Å		0.84 Å/pix.
x 416 pix.
= 349.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.21631716 - 0.53698456
Average (Standard dev.)0.0007856284 (±0.012672938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 349.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55533_msk_1.map
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Mask #2

Fileemd_55533_msk_2.map
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Additional map: 3DVA component 003 frame 000

Fileemd_55533_additional_1.map
Annotation3DVA component_003_frame_000
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Additional map: 3DVA component 003 frame 009

Fileemd_55533_additional_10.map
Annotation3DVA component_003_frame_009
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Additional map: 3DVA component 003 frame 010

Fileemd_55533_additional_11.map
Annotation3DVA component_003_frame_010
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Additional map: 3DVA component 003 frame 011

Fileemd_55533_additional_12.map
Annotation3DVA component_003_frame_011
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Additional map: 3DVA component 003 frame 012

Fileemd_55533_additional_13.map
Annotation3DVA component_003_frame_012
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Additional map: 3DVA component 003 frame 013

Fileemd_55533_additional_14.map
Annotation3DVA component_003_frame_013
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Additional map: 3DVA component 003 frame 014

Fileemd_55533_additional_15.map
Annotation3DVA component_003_frame_014
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Additional map: 3DVA component 003 frame 015

Fileemd_55533_additional_16.map
Annotation3DVA component_003_frame_015
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Additional map: 3DVA component 003 frame 016

Fileemd_55533_additional_17.map
Annotation3DVA component_003_frame_016
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Additional map: 3DVA component 003 frame 017

Fileemd_55533_additional_18.map
Annotation3DVA component_003_frame_017
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Additional map: 3DVA component 003 frame 018

Fileemd_55533_additional_19.map
Annotation3DVA component_003_frame_018
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Additional map: 3DVA component 003 frame 001

Fileemd_55533_additional_2.map
Annotation3DVA component_003_frame_001
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Additional map: 3DVA component 003 frame 019

Fileemd_55533_additional_20.map
Annotation3DVA component_003_frame_019
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Additional map: 3DVA component 003 frame 002

Fileemd_55533_additional_3.map
Annotation3DVA component_003_frame_002
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Additional map: 3DVA component 003 frame 003

Fileemd_55533_additional_4.map
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Additional map: 3DVA component 003 frame 004

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Additional map: 3DVA component 003 frame 005

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Additional map: 3DVA component 003 frame 006

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Additional map: 3DVA component 003 frame 007

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Additional map: 3DVA component 003 frame 008

Fileemd_55533_additional_9.map
Annotation3DVA component_003_frame_008
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Half map: Half-map A

Fileemd_55533_half_map_1.map
AnnotationHalf-map A
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Half map: Half-map B

Fileemd_55533_half_map_2.map
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Sample components

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Entire : ALC1/CHD1L bound to a PARylated nucleosome

EntireName: ALC1/CHD1L bound to a PARylated nucleosome
Components
  • Complex: ALC1/CHD1L bound to a PARylated nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: Widom 601 sequence
    • DNA: Widom 601 sequence
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1-like

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Supramolecule #1: ALC1/CHD1L bound to a PARylated nucleosome

SupramoleculeName: ALC1/CHD1L bound to a PARylated nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: The nucleosome was PARylated by PARP2 and HPF1 before addition of ALC1.
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 305 KDa

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.403062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Chromodomain-helicase-DNA-binding protein 1-like

MacromoleculeName: Chromodomain-helicase-DNA-binding protein 1-like / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.906766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFLLRLHTEG RAEAARVQEQ DLRQWGLTGI HLRSYQLEGV NWLAQRFHCQ NGCILGDEMG LGKTCQTIAL FIYLAGRLND EGPFLILCP LSVLSNWKEE MQRFAPGLSC VTYAGDKEER ACLQQDLKQE SRFHVLLTTY EICLKDASFL KSFPWSVLVV D EAHRLKNQ ...String:
MFLLRLHTEG RAEAARVQEQ DLRQWGLTGI HLRSYQLEGV NWLAQRFHCQ NGCILGDEMG LGKTCQTIAL FIYLAGRLND EGPFLILCP LSVLSNWKEE MQRFAPGLSC VTYAGDKEER ACLQQDLKQE SRFHVLLTTY EICLKDASFL KSFPWSVLVV D EAHRLKNQ SSLLHKTLSE FSVVFSLLLT GTPIQNSLQE LYSLLSFVEP DLFSKEEVGD FIQRYQDIEK ESESASELHK LL QPFLLRR VKAEVATELP KKTEVVIYHG MSALQKKYYK AILMKDLDAF ENETAKKVKL QNILSQLRKC VDHPYLFDGV EPE PFEVGD HLTEASGKLH LLDKLLAFLY SGGHRVLLFS QMTQMLDILQ DYMDYRGYSY ERVDGSVRGE ERHLAIKNFG QQPI FVFLL STRAGGVGMN LTAADTVIFV DSDFNPQNDL QAAARAHRIG QNKSVKVIRL IGRDTVEEIV YRKAASKLQL TNMII EGGH FTLGAQKPAA DADLQLSEIL KFGLDKLLAS EGSTMDEIDL ESILGETKDG QWVSDALPAA EGGSRDQEEG KNHMYL FEG KDYSKEPSKE DRKSFEQLVN LQKTLLEKAS QEGRSLRNKG SVLIPGLVEG STKRKRVLSP EELEDRQKKR QEAAAKR RR LIEEKKRQKE EAEHKKKMAW WESNNYQSFC LPSEESEPED LENGEESSAE LDYQDPDATS LKYVSGDVTH PQAGAEDA L IVHCVDDSGH WGRGGLFTAL EKRSAEPRKI YELAGKMKDL SLGGVLLFPV DDKESRNKGQ DLLALIVAQH RDRSNVLSG IKMAALEEGL KKIFLAAKKK KASVHLPRIG HATKGFNWYG TERLIRKHLA ARGIPTYIYY FPRSKAHHHH HH

UniProtKB: Chromodomain-helicase-DNA-binding protein 1-like

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Macromolecule #5: Widom 601 sequence

MacromoleculeName: Widom 601 sequence / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.175336 KDa
SequenceString: (DT)(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DA)(DC) (DC)(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC) ...String:
(DT)(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DA)(DC) (DC)(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG) (DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC) (DG)(DA)(DT)(DA)(DG)(DG)(DC)

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Macromolecule #6: Widom 601 sequence

MacromoleculeName: Widom 601 sequence / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.606586 KDa
SequenceString: (DG)(DC)(DC)(DT)(DA)(DT)(DC)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DG)(DC)(DC)(DT)(DA)(DT)(DC)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DG)(DA)(DT)(DG)(DG)(DT)(DC) (DA)(DC)(DC)(DT)(DA)(DG)(DA)

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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

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 33998 / Average exposure time: 2.2 sec. / Average electron dose: 45.0 e/Å2 / Details: Total dose was fractionated over 40 movie frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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: 2001174
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio reconstruction computed from the data
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 15740
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1) / Details: Local refinement in CryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8b0a

chain_id: A, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: B, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: C, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: D, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: E, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: F, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: G, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: H, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: I, source_name: PDB, initial_model_type: experimental model

8b0a

chain_id: J, source_name: PDB, initial_model_type: experimental model

1-v4

chain_id: K, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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