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- EMDB-38573: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ub... -

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Basic information

Entry
Database: EMDB / ID: EMD-38573
TitleCryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog
Map data
Sample
  • Complex: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog
    • Complex: DNMT1
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
    • Complex: DNA
      • DNA: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
      • DNA: DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3')
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
KeywordsDNA methyltransferase / protein-DNA complex / replication factor / TRANSFERASE
Function / homology
Function and homology information


chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / female germ cell nucleus ...chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / female germ cell nucleus / STAT3 nuclear events downstream of ALK signaling / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / pericentric heterochromatin / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / replication fork / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to amino acid stimulus / promoter-specific chromatin binding / NoRC negatively regulates rRNA expression / methylation / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. ...DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / 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 / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsKikuchi A / Hayashi G / Kori S / Arita K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02392, 19H05294, 19H05741,19J22030 Japan
CitationJournal: To Be Published
Title: Activation of DNMT1 by Chemically Synthesized Dual monoubiquitinated PAF15 Protein
Authors: Hayashi G / Takahashi Y / Kikuchi A / Kori S / Arita K / Murakami H
History
DepositionJan 5, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38573.png

Downloads & links

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Map

FileDownload / File: emd_38573.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 250 pix.
= 298.25 Å		1.19 Å/pix.
x 250 pix.
= 298.25 Å		1.19 Å/pix.
x 250 pix.
= 298.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.193 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.189
Minimum - Maximum-1.187701 - 1.8523676
Average (Standard dev.)-0.0003303625 (±0.027854625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 298.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38573_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38573_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38573_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ub...

EntireName: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog
Components
  • Complex: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog
    • Complex: DNMT1
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
    • Complex: DNA
      • DNA: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
      • DNA: DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3')
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ub...

SupramoleculeName: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: DNMT1

SupramoleculeName: DNMT1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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

MacromoleculeName: DNA (cytosine-5)-methyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 143.559531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPPTTPKCIQ CGQYLDDPDL KYGQHPPDAV DEPQMLTNEK LSIFDANESG FESYEALPQH KLTCFSVYCK HGHLCPIDTG LIEKNIELF FSGSAKPIYD DDPSLEGGVN GKNLGPINEW WITGFDGGEK ALIGFSTSFA EYILMDPSPE YAPIFGLMQE K IYISKIVV ...String:
GPPTTPKCIQ CGQYLDDPDL KYGQHPPDAV DEPQMLTNEK LSIFDANESG FESYEALPQH KLTCFSVYCK HGHLCPIDTG LIEKNIELF FSGSAKPIYD DDPSLEGGVN GKNLGPINEW WITGFDGGEK ALIGFSTSFA EYILMDPSPE YAPIFGLMQE K IYISKIVV EFLQSNSDST YEDLINKIET TVPPSGLNLN RFTEDSLLRH AQFVVEQVES YDEAGDSDEQ PIFLTPCMRD LI KLAGVTL GQRRAQARRQ TIRHSTREKD RGPTKATTTK LVYQIFDTFF AEQIEKDDRE DKENAFKRRR CGVCEVCQQP ECG KCKACK DMVKFGGSGR SKQACQERRC PNMAMKEADD DEEVDDNIPE MPSPKKMHQG KKKKQNKNRI SWVGEAVKTD GKKS YYKKV CIDAETLEVG DCVSVIPDDS SKPLYLARVT ALWEDSSNGQ MFHAHWFCAG TDTVLGATSD PLELFLVDEC EDMQL SYIH SKVKVIYKAP SENWAMEGGM DPESLLEGDD GKTYFYQLWY DQDYARFESP PKTQPTEDNK FKFCVSCARL AEMRQK EIP RVLEQLEDLD SRVLYYSATK NGILYRVGDG VYLPPEAFTF NIKLSSPVKR PRKEPVDEDL YPEHYRKYSD YIKGSNL DA PEPYRIGRIK EIFCPKKSNG RPNETDIKIR VNKFYRPENT HKSTPASYHA DINLLYWSDE EAVVDFKAVQ GRCTVEYG E DLPECVQVYS MGGPNRFYFL EAYNAKSKSF EDPPNHARSP GNKGKGKGKG KGKPKSQACE PSEPEIEIKL PKLRTLDVF SGCGGLSEGF HQAGISDTLW AIEMWDPAAQ AFRLNNPGST VFTEDCNILL KLVMAGETTN SRGQRLPQKG DVEMLCGGPP CQGFSGMNR FNSRTYSKFK NSLVVSFLSY CDYYRPRFFL LENVRNFVSF KRSMVLKLTL RCLVRMGYQC TFGVLQAGQY G VAQTRRRA IILAAAPGEK LPLFPEPLHV FAPRACQLSV VVDDKKFVSN ITRLSSGPFR TITVRDTMSD LPEVRNGASA LE ISYNGEP QSWFQRQLRG AQYQPILRDH ICKDMSALVA ARMRHIPLAP GSDWRDLPNI EVRLSDGTMA RKLRYTHHDR KNG RSSSGA LRGVCSCVEA GKACDPAARQ FNTLIPWCLP HTGNRHNHWA GLYGRLEWDG FFSTTVTNPE PMGKQGRVLH PEQH RVVSV RECARSQGFP DTYRLFGNIL DKHRQVGNAV PPPLAKAIGL EIKLCMLAKA RESASAKIKE EEAAKD

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #2: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')

MacromoleculeName: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.725469 KDa
SequenceString:
(DA)(DC)(DT)(DT)(DA)(5CM)(DG)(DG)(DA)(DA) (DG)(DG)

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Macromolecule #3: DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3')

MacromoleculeName: DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.679464 KDa
SequenceString:
(DC)(DC)(DT)(DT)(DC)(EIX)(DG)(DT)(DA)(DA) (DG)(DT)

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Macromolecule #4: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 4 / 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 #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
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: 60.848 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xi9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 356895
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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