7YG4 | pdb_00007yg4

Structure of WTAP-VIRMA in the m6A writer complex

• PDB DOI: https://doi.org/10.2210/pdb7YG4/pdb
• EM Map EMD-33807: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-07-11 Released: 2022-11-23 
• Deposition Author(s): Yan, X.H., Guan, Z.Y., Tang, C., Yin, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

AI-empowered integrative structural characterization of m 6 A methyltransferase complex.

Yan, X., Pei, K., Guan, Z., Liu, F., Yan, J., Jin, X., Wang, Q., Hou, M., Tang, C., Yin, P.

(2022) Cell Res 32: 1124-1127

• PubMed: 36357785 
• DOI: https://doi.org/10.1038/s41422-022-00741-8
• Primary Citation Related Structures: 
  7YFJ, 7YG4

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Peking University, Beijing, China.
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Peking University, Beijing, China. [e-mail].
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 191.93 kDa 
• Atom Count: 7,510 
• Modeled Residue Count: 953 
• Deposited Residue Count: 1,697 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein virilizer homolog	A	1,107	Homo sapiens	Mutation(s): 0  Gene Names: VIRMA
UniProt & NIH Common Fund Data Resources
Find proteins for Q69YN4 (Homo sapiens) Explore Q69YN4  Go to UniProtKB:  Q69YN4
PHAROS:  Q69YN4 GTEx:  ENSG00000164944

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing regulator WTAP	B, C [auth E]	295	Homo sapiens	Mutation(s): 0  Gene Names: WTAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q15007 (Homo sapiens) Explore Q15007  Go to UniProtKB:  Q15007
PHAROS:  Q15007 GTEx:  ENSG00000146457

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Yan, X.H., Guan, Z.Y., Tang, C., Yin, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references
• Version 1.2: 2022-12-14
  Changes: Database references
• Version 1.3: 2024-07-03
  Changes: Data collection
• Version 1.4: 2025-06-18
  Changes: Data collection, Structure summary