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Yorodumi- EMDB-34169: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3,... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34169 | |||||||||
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Title | Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14) | |||||||||
Map data | Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14) | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Su S / Li S / Deng T / Gao M / Yin Y / Wu B / Peng C / Liu J / Ma J / Zhang K | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34169.map.gz | 50.9 MB | EMDB map data format | |
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Header (meta data) | emd-34169-v30.xml emd-34169.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_34169.png | 59.6 KB | ||
Others | emd_34169_half_map_1.map.gz emd_34169_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34169 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34169 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34169.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34169_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34169_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3,...
Entire | Name: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14) |
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Components |
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-Supramolecule #1: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3,...
Supramolecule | Name: Human m6A writer complex (WTAP, VIRMA, ZC3H13, and HAKAI, METTL3, METTL14) type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199741 |