9L4K | pdb_00009l4k

Structure of human NLRP2-TLE6-OOEP complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural assembly of the subcortical maternal complex SCMC.

Ou, G.Liu, Q.Jiao, H.Han, Z.Li, J.Min, L.Chi, P.Liu, S.Li, J.Qi, Q.Zhang, Z.Guo, L.Wang, X.Li, L.Chen, J.Hu, H.Deng, D.

(2026) Structure 34: 20-31.e7

  • DOI: https://doi.org/10.1016/j.str.2025.09.009
  • Primary Citation Related Structures: 
    9L4J, 9L4K, 9L4L

  • PubMed Abstract: 

    The subcortical maternal complex (SCMC) is essential for mammalian preimplantation development, yet how SCMC core (MATER/NLRP5, TLE6, FLOPED/OOEP) engages regulatory partners remains unclear. We determined cryo-EM structures of mouse SCMC bound to ZBED3 and human SCMC bound to NLRP2. Our structure reveals that ZBED3 interacts with all three SCMC core subunits via its zinc finger domain, with conserved residue Phe73 mediating specific contacts. In contrast, human NLRP2 only binds to the WD40 domain of TLE6 through its leucine-rich repeat (LRR) domain. Similar interactions were also confirmed for NLRP7 with TLE6. These findings were cross-validated by in vivo proximity ligation and in vitro pull-down assays. Our work proposes a paradigmatic "Lego-like" assembly model, where the SCMC core sequentially recruits different partners through diverse molecular interfaces. These findings provide critical structural insights into the SCMC's architecture and its multifaceted regulatory roles in early mammalian embryogenesis.


  • Organizational Affiliation
    • Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China; Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610041, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 21,062Homo sapiensMutation(s): 0 
Gene Names: NLRP2NALP2NBS1PAN1PYPAF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX02 (Homo sapiens)
Explore Q9NX02 
Go to UniProtKB:  Q9NX02
PHAROS:  Q9NX02
GTEx:  ENSG00000022556 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NX02
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transducin-like enhancer protein 6572Homo sapiensMutation(s): 0 
Gene Names: TLE6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H808 (Homo sapiens)
Explore Q9H808 
Go to UniProtKB:  Q9H808
PHAROS:  Q9H808
GTEx:  ENSG00000104953 
Entity Groups  
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UniProt GroupQ9H808
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Oocyte-expressed protein homolog149Homo sapiensMutation(s): 0 
Gene Names: OOEPC6orf156KHDC2OEP19
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82401959

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Data collection, Database references