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- EMDB-55534: Activation intermediate of ALC1/CHD1L bound to a PARylated nucleo... -

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Basic information

Entry
Database: EMDB / ID: EMD-55534
TitleActivation intermediate of ALC1/CHD1L bound to a PARylated nucleosome - regulatory linker segment resolved
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: ALC1
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: 2.96 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_55534.png

Downloads & links

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Map

FileDownload / File: emd_55534.map.gz / Format: CCP4 / Size: 274.6 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.)
0.84 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.41320023 - 1.0223444
Average (Standard dev.)0.0010231604 (±0.0212888)
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_55534_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_55534_half_map_1.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_55534_half_map_2.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: 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: ALC1

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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 / 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 AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / 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

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / 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 DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

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 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: ALC1

MacromoleculeName: ALC1 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
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

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 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TCTAGGTGAC CATCAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCGATAGGC

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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:
GCCTATCGAT GTATATATCT GACACGTGCC TGGAGACTAG GGAGTAATCC CCTTGGCGGT TAAAACGCGG GGGACAGCGC GTACGTGCGT TTAAGCGGTG CTAGAGCTGT CTACGACCAA TTGAGCGGCC TCGGCACCGG GATTCTGATG GTCACCTAGA

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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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 57036
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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