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- EMDB-63262: Cryo-EM structure of the chromatin remodeler Rad26 bound to the n... -

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Basic information

Entry
Database: EMDB / ID: EMD-63262
TitleCryo-EM structure of the chromatin remodeler Rad26 bound to the nucleosome at SHL6
Map data
Sample
  • Complex: Rad26-nucleosome complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (169-MER)
    • DNA: DNA (169-MER)
    • Protein or peptide: DNA repair protein
KeywordsRad26 / CSB / ERCC6 / Chromatin remodeler / DNA repair / Komagataella phaffii / Komagataella pastoris / Histone H2A / Histone H2B / Histone H3 / Histone H4 / DNA / Epigenetic / Gene regulation / cryo-EM / DNA BINDING PROTEIN
Function / homology
Function and homology information


ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / helicase activity / structural constituent of chromatin / nucleosome / site of double-strand break / protein heterodimerization activity / hydrolase activity / DNA repair / DNA binding ...ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / helicase activity / structural constituent of chromatin / nucleosome / site of double-strand break / protein heterodimerization activity / hydrolase activity / DNA repair / DNA binding / ATP binding / nucleus
Similarity search - Function
: / Rad26/CSB winged helix DNA-binding domain / : / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2A conserved site / Histone H2A signature. ...: / Rad26/CSB winged helix DNA-binding domain / : / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B / Histone H2A / Histone H4 / Histone H3 / DNA repair protein
Similarity search - Component
Biological speciesKomagataella phaffii (fungus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFukushima Y / Takizawa Y / Kinoshita C / Ogasawara M / Kagawa W / Kurumizaka H
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23KJ0485 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Science and TechnologyJPMJCR24T3 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121003 Japan
CitationJournal: To Be Published
Title: Structural basis of the nucleosome remodeling by a Cockayne syndrome B homologue Komagataella phaffii Rad26
Authors: Fukushima Y / Takizawa Y / Ogasawara M / Kinoshita C / Haruhiko E / Sekine S / Kagawa W / Kurumizaka H
History
DepositionJan 23, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63262.png

Downloads & links

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Map

FileDownload / File: emd_63262.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00516
Minimum - Maximum-0.022180118 - 0.042042878
Average (Standard dev.)0.00018344229 (±0.001451659)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63262_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63262_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63262_half_map_2.map
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 : Rad26-nucleosome complex

EntireName: Rad26-nucleosome complex
Components
  • Complex: Rad26-nucleosome complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (169-MER)
    • DNA: DNA (169-MER)
    • Protein or peptide: DNA repair protein

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Supramolecule #1: Rad26-nucleosome complex

SupramoleculeName: Rad26-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Komagataella phaffii (fungus)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Details: K. phaffii H3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 15.73038 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLASKAAR KSAPSAAGGV KKPHRYKPGT VALREIRRFQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAIGALQE SVEAYLVSLF EDTNLCAIHA KRVTIQKKDI LLARRLRGER S

UniProtKB: Histone H3

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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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 11.746771 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKSGAK RHRKILRDNI QGITKPAIRR LARRGGVKRI SALIYEEVRA VLKTFLENVI RDAVTYTEHA KRKTVTSLD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 14.202319 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGGKGK ASSAEKASTS RSSKAGLTFP VGRVHRLLRR GNYAQRIGSG APVYLTAVLE YLAAEILELA GNAARDNKKS RIIPRHLQL AIRNDEELNK LLGHVTIAQG GVLPNIQSEL LPKKSAKAKA SQEL

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 14.717857 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMAPKAEK KPASKAPAEK KPTAGKKTSS SSEPKKRSKV RKESYASYIY KVLKQTHPDT GISQKAMSIM NSFVNDIFER IASEASKLA SYNKKSTISA REIQTAVRLI LPGELSKHAV SEGTRAVTKY TSSTQA

UniProtKB: Histone H2B

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Macromolecule #7: DNA repair protein

MacromoleculeName: DNA repair protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 125.503984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSHMNEE PDDLTSLGVE LVGQDTLEHQ IASMADTAML ERDKELELKR LEKTKSQIQK WQSKQRSLES KINSRNTKIS ERERFRKEL KDIEENELKV LRDDLKEINT RLQETMKASS LKAKETLDEV EQLPNETKKD FLIRTGKITA FGSVNAFTQD N PEAPVEKS ...String:
GPLGSHMNEE PDDLTSLGVE LVGQDTLEHQ IASMADTAML ERDKELELKR LEKTKSQIQK WQSKQRSLES KINSRNTKIS ERERFRKEL KDIEENELKV LRDDLKEINT RLQETMKASS LKAKETLDEV EQLPNETKKD FLIRTGKITA FGSVNAFTQD N PEAPVEKS HQSLIAPGID DDDDYVYPGE IEEIEEIETE NESDDQAAII SSKKRKRARS IEHDDVYVNS DSTEDEYDTQ TT RQSKDEI HNIDDGDDAF YNARLNAWVT KRSQKREVDA NPDEEEWFKP HPTKQDAILD DDYRLPGDVY PALFDYQKTC VQW LWELYL QKVGGILGDE MGLGKTVQII SFIAGLHYTK KLNKPVIVVC PATVLRQWCN EFHRWWPPLR VVILHAIGTG LSGS RTSLQ NEASIEKLLE EEEYGSTKSL ASLKAESRVK ELIDSVFTRG HVIITTYVGL RIYSKHLLKR DWGYAILDEG HKIRN PNSD ISLTCKQLRT PNRVILSGTP IQNNLTELWS LFDFIFPGRL GTLPVFQNQF AIPINVGGYA NATNLQVQVG YKCAVT LKD LISPYLLRRV KADVAKDLPK KSEMVLFCKL TAPQHALYEK FLRSDELSRI LQGKRQVLYG IDILRKICNH PDLVDVH AK RRSKKDPTYG SASKSGKMQV VKKLLELWKS QGHKTLLFTQ TRQMLDILES FLERLNAKGA EEEDFVPFKF LRMDGTTS I GVRQSLVDVF NNDPSYNVFL LTTRVGGLGV NLTGANRVII YDPDWNPSTD VQARERAWRL GQKKDVTIYR LMIAGSIEE KIYHRQIFKQ FLTNKILKDP KQRRFFKMNE LQDLFTLGDP DEKGTETGDM FNGMEYNFKG TKPRHSQKLS NRERSEEPQD DLVKLAQIN GVSGLQEFDG SKDEQMDSTS RQEEELMSGL FASSGVHSAL QHDSIMDSTE PEQNEAELEA RRIAAEAANS L RESRKLAR KSKIGVPTWT GKFGSAGKIL NKQRFRDNAS GVSSSSILQS IRAKRDLDTK KKERPDFNNE DNDRKLLIRR IN DFMLVQN GYKADSQTIL NSFKEINNII LMRSMLKQIC KWDSKEKVWI LKDEYVE

UniProtKB: DNA repair protein

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Macromolecule #5: DNA (169-MER)

MacromoleculeName: DNA (169-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.951098 KDa
SequenceString: (DC)(DT)(DG)(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) ...String:
(DC)(DT)(DG)(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)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DG)(DC)(DG)(DA)(DA) (DA)(DT) (DT)(DC)(DA)(DT)(DA)(DG)(DA)

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Macromolecule #6: DNA (169-MER)

MacromoleculeName: DNA (169-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.391375 KDa
SequenceString: (DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT)(DT) (DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC)(DA) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT) (DG)(DA)(DC)(DA)(DC)(DG) ...String:
(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT)(DT) (DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC)(DA) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(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)(DC)(DA)(DG)

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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

Concentration0.101 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 59.7 e/Å2
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: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36207
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9lox:
Cryo-EM structure of the chromatin remodeler Rad26 bound to the nucleosome at SHL6

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