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- EMDB-33201: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ub... -

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Entry
Database: EMDB / ID: EMD-33201
TitleCryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)
Map data
Sample
  • Complex: DNMT1:H3Ub2:DNAmCG/fCG Ternary complex of DNMT1 with hemi methylated DNA analog and H3Ub2
    • Complex: DNA (cytosine-5)-methyltransferase 1
      • 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: ZINC ION
  • Ligand: water
KeywordsDNA methyltransferase / TRANSFERASE-DNA COMPLEX
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 / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling ...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 / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / pericentric heterochromatin / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / 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 / DNA binding / RNA 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: 2.23 Å
AuthorsOnoda H / Kikuchi A / Kori S / Yoshimi S / Yamagata A / Arita K
Funding support Japan, 4 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18H02392 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H05294 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H05741 Japan
Japan Society for the Promotion of Science (JSPS)SK201904 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for activation of DNMT1.
Authors: Amika Kikuchi / Hiroki Onoda / Kosuke Yamaguchi / Satomi Kori / Shun Matsuzawa / Yoshie Chiba / Shota Tanimoto / Sae Yoshimi / Hiroki Sato / Atsushi Yamagata / Mikako Shirouzu / Naruhiko ...Authors: Amika Kikuchi / Hiroki Onoda / Kosuke Yamaguchi / Satomi Kori / Shun Matsuzawa / Yoshie Chiba / Shota Tanimoto / Sae Yoshimi / Hiroki Sato / Atsushi Yamagata / Mikako Shirouzu / Naruhiko Adachi / Jafar Sharif / Haruhiko Koseki / Atsuya Nishiyama / Makoto Nakanishi / Pierre-Antoine Defossez / Kyohei Arita /
Abstract: DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human ...DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human DNMT1 bound to its two natural activators: hemimethylated DNA and ubiquitinated histone H3. We find that a hitherto unstudied linker, between the RFTS and CXXC domains, plays a key role for activation. It contains a conserved α-helix which engages a crucial "Toggle" pocket, displacing a previously described inhibitory linker, and allowing the DNA Recognition Helix to spring into the active conformation. This is accompanied by large-scale reorganization of the inhibitory RFTS and CXXC domains, allowing the enzyme to gain full activity. Our results therefore provide a mechanistic basis for the activation of DNMT1, with consequences for basic research and drug design.
History
DepositionApr 12, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33201.png

Downloads & links

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Map

FileDownload / File: emd_33201.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.9575444 - 3.454833
Average (Standard dev.)-0.00027549858 (±0.06966507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33201_msk_1.map
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Additional map: #1

Fileemd_33201_additional_1.map
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Half map: #2

Fileemd_33201_half_map_1.map
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Half map: #1

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Sample components

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Entire : DNMT1:H3Ub2:DNAmCG/fCG Ternary complex of DNMT1 with hemi methyla...

EntireName: DNMT1:H3Ub2:DNAmCG/fCG Ternary complex of DNMT1 with hemi methylated DNA analog and H3Ub2
Components
  • Complex: DNMT1:H3Ub2:DNAmCG/fCG Ternary complex of DNMT1 with hemi methylated DNA analog and H3Ub2
    • Complex: DNA (cytosine-5)-methyltransferase 1
      • 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: ZINC ION
  • Ligand: water

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Supramolecule #1: DNMT1:H3Ub2:DNAmCG/fCG Ternary complex of DNMT1 with hemi methyla...

SupramoleculeName: DNMT1:H3Ub2:DNAmCG/fCG Ternary complex of DNMT1 with hemi methylated DNA analog and H3Ub2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170 KDa

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Supramolecule #2: DNA (cytosine-5)-methyltransferase 1

SupramoleculeName: DNA (cytosine-5)-methyltransferase 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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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: 143.106 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: PKCIQCGQYL DDPDLKYGQH PPDAVDEPQM LTNEKLSIFD ANESGFESYE ALPQHKLTCF SVYCKHGHLC PIDTGLIEKN IELFFSGSA KPIYDDDPSL EGGVNGKNLG PINEWWITGF DGGEKALIGF STSFAEYILM DPSPEYAPIF GLMQEKIYIS K IVVEFLQS ...String:
PKCIQCGQYL DDPDLKYGQH PPDAVDEPQM LTNEKLSIFD ANESGFESYE ALPQHKLTCF SVYCKHGHLC PIDTGLIEKN IELFFSGSA KPIYDDDPSL EGGVNGKNLG PINEWWITGF DGGEKALIGF STSFAEYILM DPSPEYAPIF GLMQEKIYIS K IVVEFLQS NSDSTYEDLI NKIETTVPPS GLNLNRFTED SLLRHAQFVV EQVESYDEAG DSDEQPIFLT PCMRDLIKLA GV TLGQRRA QARRQTIRHS TREKDRGPTK ATTTKLVYQI FDTFFAEQIE KDDREDKENA FKRRRCGVCE VCQQPECGKC KAC KDMVKF GGSGRSKQAC QERRCPNMAM KEADDDEEVD DNIPEMPSPK KMHQGKKKKQ NKNRISWVGE AVKTDGKKSY YKKV CIDAE TLEVGDCVSV IPDDSSKPLY LARVTALWED SSNGQMFHAH WFCAGTDTVL GATSDPLELF LVDECEDMQL SYIHS KVKV IYKAPSENWA MEGGMDPESL LEGDDGKTYF YQLWYDQDYA RFESPPKTQP TEDNKFKFCV SCARLAEMRQ KEIPRV LEQ LEDLDSRVLY YSATKNGILY RVGDGVYLPP EAFTFNIKLS SPVKRPRKEP VDEDLYPEHY RKYSDYIKGS NLDAPEP YR IGRIKEIFCP KKSNGRPNET DIKIRVNKFY RPENTHKSTP ASYHADINLL YWSDEEAVVD FKAVQGRCTV EYGEDLPE C VQVYSMGGPN RFYFLEAYNA KSKSFEDPPN HARSPGNKGK GKGKGKGKPK SQACEPSEPE IEIKLPKLRT LDVFSGCGG LSEGFHQAGI SDTLWAIEMW DPAAQAFRLN NPGSTVFTED CNILLKLVMA GETTNSRGQR LPQKGDVEML CGGPPCQGFS GMNRFNSRT YSKFKNSLVV SFLSYCDYYR PRFFLLENVR NFVSFKRSMV LKLTLRCLVR MGYQCTFGVL QAGQYGVAQT R RRAIILAA APGEKLPLFP EPLHVFAPRA CQLSVVVDDK KFVSNITRLS SGPFRTITVR DTMSDLPEVR NGASALEISY NG EPQSWFQ RQLRGAQYQP ILRDHICKDM SALVAARMRH IPLAPGSDWR DLPNIEVRLS DGTMARKLRY THHDRKNGRS SSG ALRGVC SCVEAGKACD PAARQFNTLI PWCLPHTGNR HNHWAGLYGR LEWDGFFSTT VTNPEPMGKQ GRVLHPEQHR VVSV RECAR SQGFPDTYRL FGNILDKHRQ VGNAVPPPLA KAIGLEIKLC MLAKARESAS AKIKEEEAAK D

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: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 196 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HCl2-Amino-2-hydroxymethyl-propane-1,3-diol
250.0 mMNaClSodium chloride
5.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 seconds before plunging.
DetailsThis sample was monodisperse by Size-exclusion chromatography

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 4068 / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3798046
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Non-uniform Refinement / Number images used: 897446
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: Non-uniform Refinement
Final 3D classificationNumber classes: 3 / Avg.num./class: 845352 / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: 3D Variability
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6x9i

chain_id: A, residue_range: 730-1600, source_name: PDB, initial_model_type: experimental model

6x9i

chain_id: B, residue_range: 1-12, source_name: PDB, initial_model_type: experimental model

6x9i

chain_id: C, residue_range: 13-24, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-7xib:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)

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