7VF2

Human m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of human m6A writer complexes.

Su, S.Li, S.Deng, T.Gao, M.Yin, Y.Wu, B.Peng, C.Liu, J.Ma, J.Zhang, K.

(2022) Cell Res 32: 982-994

  • DOI: https://doi.org/10.1038/s41422-022-00725-8
  • Primary Citation of Related Structures:  
    7VF2, 7VF5

  • PubMed Abstract: 

    N 6 -methyladenosine (m 6 A) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The m 6 A "writer" consists of the catalytic subunit m 6 A-METTL complex (MAC) and the regulatory subunit m 6 A-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 m 6 A writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and m 6 A methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active m 6 A writer complex.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein virilizer homolog1,812Homo sapiensMutation(s): 0 
Gene Names: VIRMAKIAA1429MSTP054
UniProt & NIH Common Fund Data Resources
Find proteins for Q69YN4 (Homo sapiens)
Explore Q69YN4 
Go to UniProtKB:  Q69YN4
PHAROS:  Q69YN4
GTEx:  ENSG00000164944 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ69YN4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger CCCH domain-containing protein 13563Homo sapiensMutation(s): 0 
Gene Names: ZC3H13KIAA0853
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T200 (Homo sapiens)
Explore Q5T200 
Go to UniProtKB:  Q5T200
PHAROS:  Q5T200
GTEx:  ENSG00000123200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5T200
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing regulator WTAP
C, D
396Homo sapiensMutation(s): 0 
Gene Names: WTAPKIAA0105
UniProt & NIH Common Fund Data Resources
Find proteins for Q15007 (Homo sapiens)
Explore Q15007 
Go to UniProtKB:  Q15007
PHAROS:  Q15007
GTEx:  ENSG00000146457 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15007
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31971130

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection