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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 / endoplasmic reticulum localization / ooplasm / 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 / endoplasmic reticulum localization / ooplasm / establishment or maintenance of apical/basal cell polarity / spermatogonial cell division / cortical granule / positive regulation of embryonic development / positive regulation of meiotic nuclear division / apical cortex / regulation of RNA stability / regulation of establishment of protein localization / mitochondrion localization / embryonic pattern specification / establishment of spindle localization / flagellated sperm motility / epigenetic programming in the zygotic pronuclei / fertilization / 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 / sperm midpiece / positive regulation of neuron differentiation / embryo implantation / actin filament organization / animal organ morphogenesis / response to insulin / regulation of protein stability / Wnt signaling pathway / apical part of cell / positive regulation of canonical Wnt signaling pathway / intracellular protein localization / regulation of protein localization / protein-containing complex assembly / cell cortex / spermatogenesis / in utero embryonic development / protein stabilization / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular space / RNA binding / zinc ion binding / ATP binding / nucleus / membrane / cytosol / cytoplasm
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: To Be Published
Title: Structural assembly of the subcortical maternal complex SCMC
Authors: Ou, G.J. / Liu, Q.T.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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