8X7W

Structure of dimeric human SCMC complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 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 structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants.

Chi, P.Ou, G.Liu, S.Ma, Q.Lu, Y.Li, J.Li, J.Qi, Q.Han, Z.Zhang, Z.Liu, Q.Guo, L.Chen, J.Wang, X.Huang, W.Li, L.Deng, D.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01396-2
  • Primary Citation of Related Structures:  
    8X7V, 8X7W

  • PubMed Abstract: 

    The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants.


  • Organizational Affiliation

    Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
A, D
1,530Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malENLRP5
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for P59047 (Homo sapiens)
Explore P59047 
Go to UniProtKB:  P59047
GTEx:  ENSG00000171487 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP59047P0AEX9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Oocyte-expressed protein homolog
B, E
159Homo sapiensMutation(s): 0 
Gene Names: OOEP
UniProt & NIH Common Fund Data Resources
Find proteins for A6NGQ2 (Homo sapiens)
Explore A6NGQ2 
Go to UniProtKB:  A6NGQ2
GTEx:  ENSG00000203907 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6NGQ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
C, F
536Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: SMT3TLE6
UniProt & NIH Common Fund Data Resources
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Find proteins for Q9H808 (Homo sapiens)
Explore Q9H808 
Go to UniProtKB:  Q9H808
PHAROS:  Q9H808
GTEx:  ENSG00000104953 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9H808Q12306
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171211

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references