+Open data
-Basic information
Entry | Database: PDB / ID: 7yg4 | ||||||
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Title | Structure of WTAP-VIRMA in the m6A writer complex | ||||||
Components |
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Keywords | PROTEIN BINDING | ||||||
Function / homology | Function and homology information RNA N6-methyladenosine methyltransferase complex / mRNA alternative polyadenylation / : / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear body / nuclear speck ...RNA N6-methyladenosine methyltransferase complex / mRNA alternative polyadenylation / : / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear body / nuclear speck / cell cycle / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Yan, X.H. / Guan, Z.Y. / Tang, C. / Yin, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2022 Title: AI-empowered integrative structural characterization of mA methyltransferase complex. Authors: Xuhui Yan / Kai Pei / Zeyuan Guan / Feiqing Liu / Junjun Yan / Xiaohuan Jin / Qiang Wang / Mengjun Hou / Chun Tang / Ping Yin / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yg4.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yg4.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 7yg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/7yg4 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/7yg4 | HTTPS FTP |
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-Related structure data
Related structure data | 33807MC 7yfjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 123716.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VIRMA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q69YN4 |
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#2: Protein | Mass: 34107.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WTAP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15007 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: WTAP-VIRMA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 55.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197685 / Symmetry type: POINT | ||||||||||||||||||||||||
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