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- PDB-9l4j: Structure of mouse SCMCcore complex contain ZBED3 -

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Basic information

Entry
Database: PDB / ID: 9l4j
TitleStructure of mouse SCMCcore complex contain ZBED3
Components
  • Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
  • Oocyte-expressed protein homolog
  • Transducin-like enhancer protein 6
  • Zinc finger BED domain-containing protein 3
KeywordsCYTOSOLIC PROTEIN / complex
Function / homology
Function and homology information


subcortical maternal complex / establishment of organelle localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / embryonic process involved in female pregnancy / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / spermatogonial cell division ...subcortical maternal complex / establishment of organelle localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / embryonic process involved in female pregnancy / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / spermatogonial cell division / cortical granule / apical cortex / positive regulation of meiotic nuclear division / regulation of RNA stability / positive regulation of embryonic development / regulation of establishment of protein localization / embryonic pattern specification / mitochondrion localization / establishment of spindle localization / flagellated sperm motility / fertilization / epigenetic programming in the zygotic pronuclei / positive regulation of neurogenesis / positive regulation of double-strand break repair / exocytosis / replication fork processing / regulation of cell division / response to glucose / positive regulation of double-strand break repair via homologous recombination / positive regulation of neuron differentiation / embryo implantation / animal organ morphogenesis / actin filament organization / regulation of protein stability / tubulin binding / negative regulation of canonical Wnt signaling pathway / response to insulin / Wnt signaling pathway / apical part of cell / intracellular protein localization / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / regulation of protein localization / regulation of inflammatory response / protein-containing complex assembly / sperm midpiece / cell cortex / spermatogenesis / transcription regulator complex / in utero embryonic development / protein stabilization / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / : / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Zinc finger BED domain-containing protein 2/3 / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain ...Zinc finger BED domain-containing protein 2/3 / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / Zinc finger C2H2 superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Oocyte-expressed protein homolog / Zinc finger BED domain-containing protein 3 / NACHT, LRR and PYD domains-containing protein 5 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsOu, G.J. / Liu, Q.T. / Jiao, H.Z. / Han, Z. / Li, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82401959 China
CitationJournal: Structure / Year: 2026
Title: Structural assembly of the subcortical maternal complex SCMC.
Authors: Guojin Ou / Qingting Liu / Haizhan Jiao / Zhuo Han / Jinhong Li / Ling Min / Pengliang Chi / Sibei Liu / Jialu Li / Qianqian Qi / Zihan Zhang / Li Guo / Xiang Wang / Lei Li / Jing Chen / Hongli Hu / Dong Deng /
Abstract: The subcortical maternal complex (SCMC) is essential for mammalian preimplantation development, yet how SCMC (MATER/NLRP5, TLE6, FLOPED/OOEP) engages regulatory partners remains unclear. We ...The subcortical maternal complex (SCMC) is essential for mammalian preimplantation development, yet how SCMC (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 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 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.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
B: Transducin-like enhancer protein 6
D: Oocyte-expressed protein homolog
E: Zinc finger BED domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0665
Polymers174,0004
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform 4 of NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 109296.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His-tagged the full-length MATER / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlrp5, Mater, Nalp5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R1M5
#2: Protein Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 47967.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tle6, Grg6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9WVB3
#3: Protein Oocyte-expressed protein homolog / Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific ...Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific protein 19 / mOEP19 / STAT3 downstream gene and differentiation regulator


Mass: 10252.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ooep, Oep19, Sddr / Production host: Spodoptera frugiperda granulovirus / References: UniProt: Q9CWE6
#4: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 6483.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zbed3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9D0L1
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse SCMCcore complex contains mZBED3 / Type: COMPLEX
Details: the virus of MATER-mTLE6-FLOPED-mZBED3 were co-transfected to Spodoptera frugiperda cell and the complex were purified by His-MATER
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 229.09 kDa/nm / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8 / Details: 25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
225 mMTris(hydroxymethyl)aminomethaneTris1
35 mMDithiothreitolDTT1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Vitrification carried out in argon atmosphere

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 51.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1993029 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411516
ELECTRON MICROSCOPYf_angle_d0.4915591
ELECTRON MICROSCOPYf_dihedral_angle_d4.3691513
ELECTRON MICROSCOPYf_chiral_restr0.0391789
ELECTRON MICROSCOPYf_plane_restr0.0041965

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