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- EMDB-34169: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3,... -

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Basic information

Entry
Database: EMDB / ID: EMD-34169
TitleHuman m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)
Map dataHuman m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)
Sample
  • Complex: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSu S / Li S / Deng T / Gao M / Yin Y / Wu B / Peng C / Liu J / Ma J / Zhang K
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971130 China
CitationJournal: Cell Res / Year: 2022
Title: Cryo-EM structures of human mA writer complexes.
Authors: Shichen Su / Shanshan Li / Ting Deng / Minsong Gao / Yue Yin / Baixing Wu / Chao Peng / Jianzhao Liu / Jinbiao Ma / Kaiming Zhang /
Abstract: N-methyladenosine (mA) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The mA "writer" consists of the catalytic subunit mA-METTL complex (MAC) and the regulatory ...N-methyladenosine (mA) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The mA "writer" consists of the catalytic subunit mA-METTL complex (MAC) and the regulatory subunit mA-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the mA writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and mA methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active mA writer complex.
History
DepositionAug 24, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34169.png

Downloads & links

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Map

FileDownload / File: emd_34169.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.049303122 - 0.30651158
Average (Standard dev.)0.0030491925 (±0.01730067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34169_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_34169_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3,...

EntireName: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)
Components
  • Complex: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)

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Supramolecule #1: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3,...

SupramoleculeName: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14)
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199741
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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