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- EMDB-44411: CryoEM structure of DIM2-HP1-H3K9me3-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44411
TitleCryoEM structure of DIM2-HP1-H3K9me3-DNA complex
Map datasharpened map
Sample
  • Complex: DIM2-HP1-H3K9m3-DNA
    • Protein or peptide: DNA (cytosine-5-)-methyltransferase
    • Protein or peptide: Heterochromatin protein one
    • Protein or peptide: Histone H3.2
    • DNA: DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')
    • DNA: 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')
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
KeywordsDNA methyltransferase / Transferase-DNA Binding Protein-DNA complex
Function / homology
Function and homology information


organic cyclic compound binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / pericentric heterochromatin / methylated histone binding / structural constituent of chromatin / nucleosome / methylation / chromatin remodeling / protein heterodimerization activity ...organic cyclic compound binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / pericentric heterochromatin / methylated histone binding / structural constituent of chromatin / nucleosome / methylation / chromatin remodeling / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain, conserved site / Chromo domain signature. / 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. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain, conserved site / Chromo domain signature. / 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. / 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 superfamily / Bromo adjacent homology (BAH) domain / 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
Histone H3.2 / Heterochromatin protein one / DNA (cytosine-5-)-methyltransferase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsSong J / Shao Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: CryoEM structure of DIM2-HP1-H3K9me3-DNA complex
Authors: Song J / Shao Z
History
DepositionApr 4, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44411.png

Downloads & links

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Map

FileDownload / File: emd_44411.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.48012254 - 0.9714123
Average (Standard dev.)0.0002231549 (±0.023326533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_44411_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_44411_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_44411_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DIM2-HP1-H3K9m3-DNA

EntireName: DIM2-HP1-H3K9m3-DNA
Components
  • Complex: DIM2-HP1-H3K9m3-DNA
    • Protein or peptide: DNA (cytosine-5-)-methyltransferase
    • Protein or peptide: Heterochromatin protein one
    • Protein or peptide: Histone H3.2
    • DNA: DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')
    • DNA: 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')
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: DIM2-HP1-H3K9m3-DNA

SupramoleculeName: DIM2-HP1-H3K9m3-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Neurospora crassa (fungus)

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

MacromoleculeName: DNA (cytosine-5-)-methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 139.935891 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMDSPDRSH GGMFIDVPAE TMGFQEDYLD MFASVLSQGL AKEGDYAHHQ PLPAGKEECL EPIAVATTIT PSPDDPQLQL QLELEQQFQ TESGLNGVDP APAPESEDEA DLPDGFSDES PDDDFVVQRS KHITVDLPVS TLINPRSTFQ RIDENDNLVP P PQSTPERV ...String:
GSMDSPDRSH GGMFIDVPAE TMGFQEDYLD MFASVLSQGL AKEGDYAHHQ PLPAGKEECL EPIAVATTIT PSPDDPQLQL QLELEQQFQ TESGLNGVDP APAPESEDEA DLPDGFSDES PDDDFVVQRS KHITVDLPVS TLINPRSTFQ RIDENDNLVP P PQSTPERV AVEDLLKAAK AAGKNKEDYI EFELHDFNFY VNYAYHPQEM RPIQLVATKV LHDKYYFDGV LKYGNTKHYV TG MQVLELP VGNYGASLHS VKGQIWVRSK HNAKKEIYYL LKKPAFEYQR YYQPFLWIAD LGKHVVDYCT RMVERKREVT LGC FKSDFI QWASKAHGKS KAFQNWRAQH PSDDFRTSVA ANIGYIWKEI NGVAGAKRAA GDQLFRELMI VKPGQYFRQE VPPG PVVTE GDRTVAATIV TPYIKECFGH MILGKVLRLA GEDAEKEKEV KLAKRLKIEN KNATKADTKD DMKNDTATES LPTPL RSLP VQVLEATPIE SDIVSIVSSD LPPSENNPPP LTNGSVKPKA KANPKPKPST QPLHAAHVKY LSQELVNKIK VGDVIS TPR DDSSNTDTKW KPTDTDDHRW FGLVQRVHTA KTKSSGRGLN SKSFDVIWFY RPEDTPCCAM KYKWRNELFL SNHCTCQ EG HHARVKGNEV LAVHPVDWFG TPESNKGEFF VRQLYESEQR RWITLQKDHL TCYHNQPPKP PTAPYKPGDT VLATLSPS D KFSDPYEVVE YFTQGEKETA FVRLRKLLRR RKVDRQDAPA NELVYTEDLV DVRAERIVGK CIMRCFRPDE RVPSPYDRG GTGNMFFITH RQDHGRCVPL DTLPPTLRQG FNPLGNLGKP KLRGMDLYCG GGNFGRGLEE GGVVEMRWAN DIWDKAIHTY MANTPDPNK TNPFLGSVDD LLRLALEGKF SDNVPRPGEV DFIAAGSPCP GFSLLTQDKK VLNQVKNQSL VASFASFVDF Y RPKYGVLE NVSGIVQTFV NRKQDVLSQL FCALVGMGYQ AQLILGDAWA HGAPQSRERV FLYFAAPGLP LPDPPLPSHS HY RVKNRNI GFLCNGESYV QRSFIPTAFK FVSAGEGTAD LPKIGDGKPD ACVRFPDHRL ASGITPYIRA QYACIPTHPY GMN FIKAWN NGNGVMSKSD RDLFPSEGKT RTSDASVGWK RLNPKTLFPT VTTTSNPSDA RMGPGLHWDE DRPYTVQEMR RAQG YLDEE VLVGRTTDQW KLVGNSVSRH MALAIGLKFR EAWLGTLYD

UniProtKB: DNA (cytosine-5-)-methyltransferase

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Macromolecule #2: Heterochromatin protein one

MacromoleculeName: Heterochromatin protein one / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 30.489086 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMPYDPSAL SDEEAASSVE LDTRSATSSS KKQSRDKKSV KYTIPEPEDF EDEEQNGDGA DEGGEDDEEG DEEEEDVYVV EKILDHMLN DDNEPLFLVK WEGYEKKSDQ TWEPEDTLIE GASERLKEYF TKIGGREKIF EASAAAQKIK KRGRPSSNSG T PQASSNKR ...String:
GSMPYDPSAL SDEEAASSVE LDTRSATSSS KKQSRDKKSV KYTIPEPEDF EDEEQNGDGA DEGGEDDEEG DEEEEDVYVV EKILDHMLN DDNEPLFLVK WEGYEKKSDQ TWEPEDTLIE GASERLKEYF TKIGGREKIF EASAAAQKIK KRGRPSSNSG T PQASSNKR SRKNGDHPLN SEEPQTAKNA AWKPPAGSWE EHIAQLDACE DEDTHKLMVY LTWKNGHKTQ HTTDVIYKRC PQ KMLQFYE RHVRIIKRDP DSEDREGSVS Q

UniProtKB: Heterochromatin protein one

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 2.791302 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ARTKQTAR(M3L)S TGGKAPRKQL ATKAW

UniProtKB: Histone H3.2

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

MacromoleculeName: DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 5.709714 KDa
SequenceString:
(DA)(DG)(DT)(DA)(DG)(DG)(DA)(DG)(DG)(DA) (DG)(DG)(DA)(DG)(DT)(DA)(DG)(DT)

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Macromolecule #5: DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*...

MacromoleculeName: 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')
type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 5.323441 KDa
SequenceString:
(DA)(DC)(DT)(DA)(DC)(DT)(PYO)(DC)(DT)(DC) (DC)(DT)(DC)(DC)(DT)(DA)(DC)(DT)

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Macromolecule #6: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128667
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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