9L4J | pdb_00009l4j

Structure of mouse SCMCcore complex contain ZBED3


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 1.1 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5963Mus musculusMutation(s): 0 
Gene Names: Nlrp5MaterNalp5
UniProt
Find proteins for Q9R1M5 (Mus musculus)
Explore Q9R1M5 
Go to UniProtKB:  Q9R1M5
Entity Groups  
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UniProt GroupQ9R1M5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transducin-like enhancer protein 6427Mus musculusMutation(s): 0 
Gene Names: Tle6Grg6
UniProt
Find proteins for Q9WVB3 (Mus musculus)
Explore Q9WVB3 
Go to UniProtKB:  Q9WVB3
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UniProt GroupQ9WVB3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Oocyte-expressed protein homologC [auth D]89Mus musculusMutation(s): 0 
Gene Names: OoepOep19Sddr
UniProt
Find proteins for Q9CWE6 (Mus musculus)
Explore Q9CWE6 
Go to UniProtKB:  Q9CWE6
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UniProt GroupQ9CWE6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger BED domain-containing protein 3D [auth E]56Mus musculusMutation(s): 0 
Gene Names: Zbed3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D0L1 (Mus musculus)
Explore Q9D0L1 
Go to UniProtKB:  Q9D0L1
IMPC:  MGI:1919364
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UniProt GroupQ9D0L1
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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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