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- PDB-8skz: Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome -

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Basic information

Entry
Database: PDB / ID: 8skz
TitleCryo-EM structure of DDM1-HELLS chimera bound to the nucleosome
Components
  • (DNA (192-MER)) x 2
  • ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsTRANSLOCASE / helicase / chimera / complex
Function / homology
Function and homology information


chromosomal DNA methylation maintenance following DNA replication / DNA-mediated transformation / urogenital system development / retrotransposition / lymphocyte proliferation / pericentric heterochromatin formation / TGFBR3 expression / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of intrinsic apoptotic signaling pathway ...chromosomal DNA methylation maintenance following DNA replication / DNA-mediated transformation / urogenital system development / retrotransposition / lymphocyte proliferation / pericentric heterochromatin formation / TGFBR3 expression / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of intrinsic apoptotic signaling pathway / chromosome, centromeric region / pericentric heterochromatin / DNA helicase activity / cellular response to leukemia inhibitory factor / epigenetic regulation of gene expression / kidney development / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / hydrolase activity / chromatin remodeling / protein heterodimerization activity / cell division / apoptotic process / chromatin binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B 1.1 / Histone H3.2 / Histone H2A / Lymphoid-specific helicase / ATP-dependent DNA helicase DDM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Homo sapiens (human)
Xenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNartey, W. / Williams, G.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04327 Canada
CitationJournal: To Be Published
Title: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
Authors: Nartey, W. / Williams, G.J.
History
DepositionApr 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
B: Histone H3.2
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: Histone H4
J: DNA (192-MER)
K: DNA (192-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,86913
Polymers323,37611
Non-polymers4932
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules ABECGDHFI

#1: Protein ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera


Mass: 93326.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag,This protein is a chimera of Arabidopsis ...Details: This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag,This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag,This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag
Source: (gene. exp.) Arabidopsis thaliana (thale cress), (gene. exp.) Homo sapiens (human)
Gene: DDM1, HELLS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XFH4, UniProt: Q9NRZ9
#2: Protein Histone H3.2 / Histone H3


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#3: Protein Histone H2A


Mass: 14381.696 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#5: Protein Histone H4


Mass: 12276.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398084 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LTD2

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DNA chain , 2 types, 2 molecules JK

#6: DNA chain DNA (192-MER)


Mass: 59004.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: DNA chain DNA (192-MER)


Mass: 59546.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Arabidopsis thaliana (thale cress)3702
31Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.95 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7808

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC3.3.2CTF correction
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84067 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 139.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004618158
ELECTRON MICROSCOPYf_angle_d0.579125883
ELECTRON MICROSCOPYf_chiral_restr0.04152936
ELECTRON MICROSCOPYf_plane_restr0.00352182
ELECTRON MICROSCOPYf_dihedral_angle_d24.25437338

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