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- EMDB-13065: Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-13065
TitleCryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome
Map dataMain map
Sample
  • Complex: ALC1/CHD1L bound to a PARylated nucleosome
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1-like
    • 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: DNA (149-MER) Widom 601 sequence
    • DNA: DNA (149-MER) Widom 601 sequence
KeywordsALC1 / CHD1L / chromatin remodeler / DNA damage response / nucleosome / poly(ADP-ribose) / DNA BINDING PROTEIN
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / poly-ADP-D-ribose modification-dependent protein binding / site of DNA damage / DNA helicase activity / nucleosome binding / histone reader 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 ...ATP-dependent chromatin remodeler activity / poly-ADP-D-ribose modification-dependent protein binding / site of DNA damage / DNA helicase activity / nucleosome binding / histone reader 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 / nucleosome / site of double-strand break / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromatin remodeling / protein heterodimerization activity / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / DNA repair / nucleotide binding / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
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 H2A / Histone 2A / 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 / 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 / Macro domain profile. / 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: 4.8 Å
AuthorsBacic L / Gaullier G
Funding support Sweden, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)714068 Sweden
Knut and Alice Wallenberg Foundation019.0306 Sweden
Swedish Research Council2019-03534 Sweden
Cancerfonden19 0055 Pj Sweden
CitationJournal: Elife / Year: 2021
Title: Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome.
Authors: Luka Bacic / Guillaume Gaullier / Anton Sabantsev / Laura C Lehmann / Klaus Brackmann / Despoina Dimakou / Mario Halic / Graeme Hewitt / Simon J Boulton / Sebastian Deindl /
Abstract: The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a ...The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and suggest that ALC1 preferentially slides nucleosomes away from DNA breaks.
History
DepositionJun 10, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
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  • Surface view with fitted model
  • Atomic models: PDB-7otq
  • Surface level: 0.15
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13065.png

Downloads & links

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Map

FileDownload / File: emd_13065.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430.08 Å		1.08 Å/pix.
x 400 pix.
= 430.08 Å		1.08 Å/pix.
x 400 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.39473256 - 0.8218156
Average (Standard dev.)0.00007375511 (±0.022399737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.07521.07521.0752
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3950.8220.000

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Supplemental data

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Mask #1

Fileemd_13065_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_13065_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_13065_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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: Chromodomain-helicase-DNA-binding protein 1-like
    • 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: DNA (149-MER) Widom 601 sequence
    • DNA: DNA (149-MER) Widom 601 sequence

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

MacromoleculeName: Chromodomain-helicase-DNA-binding protein 1-like / type: protein_or_peptide / ID: 1 / Details: C-terminal 6-His tag. / 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 #2: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 2 / 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 #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / 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 #4: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 4 / 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 #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / 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 #6: DNA (149-MER) Widom 601 sequence

MacromoleculeName: DNA (149-MER) Widom 601 sequence / type: dna / ID: 6 / 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 #7: DNA (149-MER) Widom 601 sequence

MacromoleculeName: DNA (149-MER) Widom 601 sequence / type: dna / ID: 7 / 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 / Details: Current 20 mA.
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: 26747 / 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
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: 3321590
Startup modelType of model: INSILICO MODEL
In silico model: Synthetic map at 30 A resolution generated from PDB entry 3LZ0 (free nucleosome) with the molmap command in ChimeraX.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Details: Non-uniform refinement in cryoSPARC 3.2.0. / Number images used: 5487
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) / Details: Non-uniform refinement in cryoSPARC.
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 3.2.0)
Details: The final set of 5487 particles used for non-uniform refinement in cryoSPARC were identified by GMM clustering of results from 3D variability analysis in cryoSPARC.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6ryr

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

6jyl

chain_id: K, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Real-space CC
Output model

PDB-7otq:
Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome

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