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- EMDB-50795: Human DNA methyltransferase 1 in non-productive complex with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-50795
TitleHuman DNA methyltransferase 1 in non-productive complex with DNA
Map datacryo-EM single particle map of HsDNMT1:DNA
Sample
  • Complex: Human DNA methyltransferase 1 in non-productive complex with DNA in presence of inhibitor GSK3852279B
KeywordsDNA methylation / methyltransferase / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.11 Å
AuthorsDe I / Weidenhausen J / Mueller CW / Concha N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS One / Year: 2024
Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy.
Authors: Inessa De / Jonas Weidenhausen / Nestor Concha / Christoph W Müller /
Abstract: DNMT1 is an essential DNA methyltransferase that catalyzes the transfer of methyl groups to CpG islands in DNA and generates a prominent epigenetic mark. The catalytic activity of DNMT1 relies on its ...DNMT1 is an essential DNA methyltransferase that catalyzes the transfer of methyl groups to CpG islands in DNA and generates a prominent epigenetic mark. The catalytic activity of DNMT1 relies on its conformational plasticity and ability to change conformation from an auto-inhibited to an activated state. Here, we present four cryo-EM reconstructions of apo DNMT1 and DNTM1: non-productive DNA, DNTM1: H3Ub2-peptide, DNTM1: productive DNA complexes. Our structures demonstrate the flexibility of DNMT1's N-terminal regulatory domains during the transition from an apo 'auto-inhibited' to a DNA-bound 'non-productive' and finally a DNA-bound 'productive' state of DNMT1. Furthermore, we address the regulation of DNMT1's methyltransferase activity by a DNMT1-selective small-molecule inhibitor and ubiquitinated histone H3. We observe that DNMT1 binds DNA in a 'non-productive' state despite the presence of the inhibitor and present the cryo-EM reconstruction of full-length DNMT1 in complex with a di-ubiquitinated H3 peptide analogue. Taken together, our results provide structural insights into the reaction cycle of DNMT1.
History
DepositionJun 26, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50795.png

Downloads & links

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Map

FileDownload / File: emd_50795.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM single particle map of HsDNMT1:DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 247.68 Å		0.65 Å/pix.
x 384 pix.
= 247.68 Å		0.65 Å/pix.
x 384 pix.
= 247.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.061
Minimum - Maximum-0.07398229 - 0.4216158
Average (Standard dev.)0.0010255442 (±0.014564275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 247.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map A

Fileemd_50795_half_map_1.map
Annotationhalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human DNA methyltransferase 1 in non-productive complex with DNA ...

EntireName: Human DNA methyltransferase 1 in non-productive complex with DNA in presence of inhibitor GSK3852279B
Components
  • Complex: Human DNA methyltransferase 1 in non-productive complex with DNA in presence of inhibitor GSK3852279B

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Supramolecule #1: Human DNA methyltransferase 1 in non-productive complex with DNA ...

SupramoleculeName: Human DNA methyltransferase 1 in non-productive complex with DNA in presence of inhibitor GSK3852279B
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.4 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE
Details0.4 mg/mL DNMT1 with DNMT1:DNA:SAM:GSK3852279B ratio of 1:1.5:20:10. Premixed on ice and then vitrified.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 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: 5.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20006
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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