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- PDB-9baq: CryoEM structure of DIM2-HP1-H3K9me3-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9baq
TitleCryoEM structure of DIM2-HP1-H3K9me3-DNA complex
Components
  • DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3')
  • DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')
  • DNA (cytosine-5-)-methyltransferase
  • Heterochromatin protein one
  • Histone H3.2
KeywordsTransferase/DNA Binding Protein/DNA / DNA methyltransferase / Transferase-DNA Binding Protein-DNA complex
Function / homology
Function and homology information


regulation of biosynthetic process / DNA (cytosine-5-)-methyltransferase activity / : / DNA (cytosine-5-)-methyltransferase / negative regulation of gene expression via chromosomal CpG island methylation / heterochromatin / structural constituent of chromatin / nucleosome / methylation / chromatin remodeling ...regulation of biosynthetic process / DNA (cytosine-5-)-methyltransferase activity / : / DNA (cytosine-5-)-methyltransferase / negative regulation of gene expression via chromosomal CpG island methylation / heterochromatin / structural constituent of chromatin / nucleosome / methylation / chromatin remodeling / protein heterodimerization activity / chromatin binding / DNA binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / : / Chromo domain, conserved site / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / Chromo domain signature. ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / : / Chromo domain, conserved site / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / Chromo domain signature. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Histone H3.2 / Heterochromatin protein one / DNA (cytosine-5-)-methyltransferase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsSong, J. / Shao, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation.
Authors: Zengyu Shao / Jiuwei Lu / Nelli Khudaverdyan / Jikui Song /
Abstract: Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. ...Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora. The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / em_admin ...chem_comp / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5-)-methyltransferase
B: Heterochromatin protein one
C: Heterochromatin protein one
D: Histone H3.2
F: Histone H3.2
G: DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')
H: DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,9809
Polymers217,5307
Non-polymers4502
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 , 2 types, 3 molecules ABC

#1: Protein DNA (cytosine-5-)-methyltransferase


Mass: 139935.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: dim-2, GE21DRAFT_10473 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96W73, DNA (cytosine-5-)-methyltransferase
#2: Protein Heterochromatin protein one


Mass: 30489.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: 49D12.150, hpo, GE21DRAFT_9232 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q870N8

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Protein/peptide , 1 types, 2 molecules DF

#3: Protein/peptide Histone H3.2


Mass: 2791.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5MYA4

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DNA chain , 2 types, 2 molecules GH

#4: DNA chain DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')


Mass: 5709.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: DNA chain DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3')


Mass: 5323.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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: DIM2-HP1-H3K9m3-DNA / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Neurospora crassa (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128667 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310070
ELECTRON MICROSCOPYf_angle_d0.52913847
ELECTRON MICROSCOPYf_dihedral_angle_d18.481672
ELECTRON MICROSCOPYf_chiral_restr0.0391496
ELECTRON MICROSCOPYf_plane_restr0.0041666

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