9L4J | pdb_00009l4j

Structure of mouse SCMCcore complex contain ZBED3

• PDB DOI: https://doi.org/10.2210/pdb9L4J/pdb
• EM Map EMD-62813: EMDB EMDataResource

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda, Spodoptera frugiperda granulovirus
• Mutation(s): No 


• Deposited: 2024-12-20 Released: 2025-10-01 
• Deposition Author(s): Ou, G.J., Liu, Q.T., Jiao, H.Z., Han, Z., Li, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

Structural assembly of the subcortical maternal complex SCMC

Ou, G.J., Liu, Q.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 174.07 kDa 
• Atom Count: 11,293 
• Modeled Residue Count: 1,430 
• Deposited Residue Count: 1,535 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5	A	963	Mus musculus	Mutation(s): 0  Gene Names: Nlrp5, Mater, Nalp5
UniProt
Find proteins for Q9R1M5 (Mus musculus) Explore Q9R1M5  Go to UniProtKB:  Q9R1M5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transducin-like enhancer protein 6	B	427	Mus musculus	Mutation(s): 0  Gene Names: Tle6, Grg6
UniProt
Find proteins for Q9WVB3 (Mus musculus) Explore Q9WVB3  Go to UniProtKB:  Q9WVB3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Oocyte-expressed protein homolog	C [auth D]	89	Mus musculus	Mutation(s): 0  Gene Names: Ooep, Oep19, Sddr
UniProt
Find proteins for Q9CWE6 (Mus musculus) Explore Q9CWE6  Go to UniProtKB:  Q9CWE6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger BED domain-containing protein 3	D [auth E]	56	Mus musculus	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Ou, G.J., Liu, Q.T., Jiao, H.Z., Han, Z., Li, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82401959

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release