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- EMDB-13070: cryoDRGN graph traversal of the ALC1 - PARylated nucleosome compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-13070
TitlecryoDRGN graph traversal of the ALC1 - PARylated nucleosome complex particle distribution
Map datavol_000.mrc from cryoDRGN graph traversal.
Sample
  • Complex: ALC1/CHD1L bound to a PARylated nucleosome
    • Complex: ALC1/CHD1L
      • Protein or peptide: ALC1/CHD1L
    • Complex: Histone
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: Widom 601 sequence
      • DNA: Widom 601 sequence
      • DNA: Widom 601 sequence
Function / homology
Function and homology information


poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / site of DNA damage / nucleosome binding / DNA helicase activity / 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 ...poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / site of DNA damage / nucleosome binding / DNA helicase activity / 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 / 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 / plasma membrane / cytosol
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 1-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Histone H2B signature. / Histone H2B / Histone H2B ...Chromodomain-helicase-DNA-binding protein 1-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Helicase conserved C-terminal domain / 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 speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsBacic L / Gaullier G / Deindl S
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-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13070.png

Downloads & links

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Map

FileDownload / File: emd_13070.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationvol_000.mrc from cryoDRGN graph traversal.
Voxel sizeX=Y=Z: 1.68 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.014
Minimum - Maximum-0.19022673 - 0.09633083
Average (Standard dev.)0.0012134946 (±0.00696156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z215.040215.040215.040
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1900.0960.001

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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
    • Complex: ALC1/CHD1L
      • Protein or peptide: ALC1/CHD1L
    • Complex: Histone
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: Widom 601 sequence
      • DNA: Widom 601 sequence
      • DNA: 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.
Molecular weightTheoretical: 305 KDa

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Supramolecule #2: ALC1/CHD1L

SupramoleculeName: ALC1/CHD1L / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: ALC1/CHD1L
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5 / Details: Histone
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Widom 601 sequence

SupramoleculeName: Widom 601 sequence / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7 / Details: Widom 601 sequence
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: ALC1/CHD1L

MacromoleculeName: ALC1/CHD1L / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFLLRLHTEG RAEAARVQEQ DLRQWGLTGI HLRSYQLEGV NWLAQRFHCQ NGCILGDEMG LGKTCQTIAL FIYLAGRLND EGPFLILCPL SVLSNWKEEM QRFAPGLSCV TYAGDKEERA CLQQDLKQES RFHVLLTTYE ICLKDASFLK SFPWSVLVVD EAHRLKNQSS ...String:
MFLLRLHTEG RAEAARVQEQ DLRQWGLTGI HLRSYQLEGV NWLAQRFHCQ NGCILGDEMG LGKTCQTIAL FIYLAGRLND EGPFLILCPL SVLSNWKEEM QRFAPGLSCV TYAGDKEERA CLQQDLKQES RFHVLLTTYE ICLKDASFLK SFPWSVLVVD EAHRLKNQSS LLHKTLSEFS VVFSLLLTGT PIQNSLQELY SLLSFVEPDL FSKEEVGDFI QRYQDIEKES ESASELHKLL QPFLLRRVKA EVATELPKKT EVVIYHGMSA LQKKYYKAIL MKDLDAFENE TAKKVKLQNI LSQLRKCVDH PYLFDGVEPE PFEVGDHLTE ASGKLHLLDK LLAFLYSGGH RVLLFSQMTQ MLDILQDYMD YRGYSYERVD GSVRGEERHL AIKNFGQQPI FVFLLSTRAG GVGMNLTAAD TVIFVDSDFN PQNDLQAAAR AHRIGQNKSV KVIRLIGRDT VEEIVYRKAA SKLQLTNMII EGGHFTLGAQ KPAADADLQL SEILKFGLDK LLASEGSTMD EIDLESILGE TKDGQWVSDA LPAAEGGSRD QEEGKNHMYL FEGKDYSKEP SKEDRKSFEQ LVNLQKTLLE KASQEGRSLR NKGSVLIPGL VEGSTKRKRV LSPEELEDRQ KKRQEAAAKR RRLIEEKKRQ KEEAEHKKKM AWWESNNYQS FCLPSEESEP EDLENGEESS AELDYQDPDA TSLKYVSGDV THPQAGAEDA LIVHCVDDSG HWGRGGLFTA LEKRSAEPRK IYELAGKMKD LSLGGVLLFP VDDKESRNKG QDLLALIVAQ HRDRSNVLSG IKMAALEEGL KKIFLAAKKK KASVHLPRIG HATKGFNWYG TERLIRKHLA ARGIPTYIYY FPRSKAHHHH HH

+
Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

+
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

+
Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGG VTIAQGGVLP NIQSVLLPKK TESAKSAKSK

+
Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

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Macromolecule #6: Widom 601 sequence

MacromoleculeName: Widom 601 sequence / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
AATCGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTTA AGCGGTGCTA GAGCTGTCTA CGACCAATTG AGCGGCCTCG GCACCGGGAT TCTGATGGTC ACCTAGA

+
Macromolecule #7: Widom 601 sequence

MacromoleculeName: Widom 601 sequence / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TCTAGGTGAC CATCAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCGATT

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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 - 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
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.9)
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 reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER
Details: cryoDRGN does not report any measure of resolution.
Number images used: 43698
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: NOT APPLICABLE / Details: Analysis of heterogeneity with cryoDRGN.
Final 3D classificationDetails: Analysis of the heterogeneity in a set of 43698 particles with cryoDRGN.

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