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- PDB-9lox: Cryo-EM structure of the chromatin remodeler Rad26 bound to the n... -

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Basic information

Entry
Database: PDB / ID: 9lox
TitleCryo-EM structure of the chromatin remodeler Rad26 bound to the nucleosome at SHL6
Components
  • (DNA (169-MER)) x 2
  • DNA repair protein
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN / Rad26 / CSB / ERCC6 / Chromatin remodeler / DNA repair / Komagataella phaffii / Komagataella pastoris / Histone H2A / Histone H2B / Histone H3 / Histone H4 / DNA / Epigenetic / Gene regulation / cryo-EM
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
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H2A / Histone H4 / Histone H3 / DNA repair protein
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFukushima, Y. / Takizawa, Y. / Kinoshita, C. / Ogasawara, M. / Kagawa, W. / Kurumizaka, H.
Funding support Japan, 8items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (169-MER)
J: DNA (169-MER)
K: DNA repair protein


Theoretical massNumber of molelcules
Total (without water)342,64111
Polymers342,64111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3


Mass: 15730.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: K. phaffii H3 / Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_c034_0036, PAS_chr2-2_0199 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R2J7
#2: Protein Histone H4


Mass: 11746.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_c034_0035, PAS_chr2-2_0200 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R2J6
#3: Protein Histone H2A


Mass: 14202.319 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0429 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0M8
#4: Protein Histone H2B


Mass: 14717.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0428 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0M7
#7: Protein DNA repair protein / Chromatin remodeler Rad26 (CSB homologue)


Mass: 125503.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: RAD26, PP7435_Chr2-0651 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QSG0

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (169-MER)


Mass: 51951.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (169-MER)


Mass: 52391.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rad26-nucleosome complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Komagataella phaffii (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.101 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm
Image recordingElectron dose: 59.7 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36207 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416897
ELECTRON MICROSCOPYf_angle_d0.62624049
ELECTRON MICROSCOPYf_dihedral_angle_d29.4654257
ELECTRON MICROSCOPYf_chiral_restr0.0382727
ELECTRON MICROSCOPYf_plane_restr0.0052056

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