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- EMDB-62813: Structure of mouse SCMCcore complex contain ZBED3 -

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Basic information

Entry
Database: EMDB / ID: EMD-62813
TitleStructure of mouse SCMCcore complex contain ZBED3
Map data
Sample
  • Complex: mouse SCMCcore complex contains mZBED3
    • Protein or peptide: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Zinc finger BED domain-containing protein 3
  • Ligand: ZINC ION
Keywordscomplex / CYTOSOLIC PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsOu GJ / Liu QT / Jiao HZ / Han Z / Li JH
Funding support China, 1 items
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, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62813.png

Downloads & links

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Map

FileDownload / File: emd_62813.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0131
Minimum - Maximum-0.030001743 - 0.063985676
Average (Standard dev.)-0.0000028831173 (±0.0017083964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62813_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62813_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse SCMCcore complex contains mZBED3

EntireName: mouse SCMCcore complex contains mZBED3
Components
  • Complex: mouse SCMCcore complex contains mZBED3
    • Protein or peptide: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Zinc finger BED domain-containing protein 3
  • Ligand: ZINC ION

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Supramolecule #1: mouse SCMCcore complex contains mZBED3

SupramoleculeName: mouse SCMCcore complex contains mZBED3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: the virus of MATER-mTLE6-FLOPED-mZBED3 were co-transfected to Spodoptera frugiperda cell and the complex were purified by His-MATER
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 229.09 kDa/nm

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Macromolecule #1: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5

MacromoleculeName: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
type: protein_or_peptide / ID: 1 / Details: His-tagged the full-length MATER / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 109.296773 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DLQDYKAHVI AKFDTSVDLH YDSPEMKLLS DAFKPYQKTF QPHTIILHGR PGVGKSALAR SIVLGWAQGK LFQKMSFVIF FSVREIKWT EKSSLAQLIA KECPDSWDLV TKIMSQPERL LFVIDGLDDM DSVLQHDDMT LSRDWKDEQP IYILMYSLLR K ALLPQSFL ...String:
DLQDYKAHVI AKFDTSVDLH YDSPEMKLLS DAFKPYQKTF QPHTIILHGR PGVGKSALAR SIVLGWAQGK LFQKMSFVIF FSVREIKWT EKSSLAQLIA KECPDSWDLV TKIMSQPERL LFVIDGLDDM DSVLQHDDMT LSRDWKDEQP IYILMYSLLR K ALLPQSFL IITTRNTGLE KLKSMVVSPL YILVEGLSAS RRSQLVLENI SNESDRIQVF HSLIENHQLF DQCQAPSVCS LV CEALQLQ KKLGKRCTLP CQTLTGLYAT LVFHQLTLKR PSQSALSQEE QITLVGLCMM AAEGVWTMRS VFYDDDLKNY SLK ESEILA LFHMNILLQV GHNSEQCYVF SHLSLQDFFA ALYYVLEGLE EWNQHFCFIE NQRSIMEVKR TDDTRLLGMK RFLF GLMNK DILKTLEVLF EYPVIPTVEQ KLQHWVSLIA QQVNGTSPMD TLDAFYCLFE SQDEEFVGGA LKRFQEVWLL INQKM DLKV SSYCLKHCQN LKAIRVDIRD LLSVDNTLEL CPVVTVQETQ CKPLLMEWWG NFCSVLGSLR NLKELDLGDS ILSQRA MKI LCLELRNQSC RIQKLTFKSA EVVSGLKHLW KLLFSNQNLK YLNLGNTPMK DDDMKLACEA LKHPKCSVET LRLDSCE LT IIGYEMISTL LISTTRLKCL SLAKNRVGVK SMISLGNALS SSMCLLQKLI LDNCGLTPAS CHLLVSALFS NQNLTHLC L SNNSLGTEGV QQLCQFLRNP ECALQRLILN HCNIVDDAYG FLAMRLANNT KLTHLSLTMN PVGDGAMKLL CEALKEPTC YLQELELVDC QLTQNCCEDL ACMITTTKHL KSLDLGNNAL GDKGVITLCE GLKQSSSSLR RLGLGACKLT SNCCEALSLA ISCNPHLNS LNLVKNDFST SGMLKLCSAF QCPVSNLGII GLWKQEYYAR VRRQLEEVEF VKPHVVIDGD WYASDEDDRN W WKN

UniProtKB: NACHT, LRR and PYD domains-containing protein 5

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Macromolecule #2: Transducin-like enhancer protein 6

MacromoleculeName: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 47.967273 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PQFCQGFLIQ GLWELFMDSR QKNQQEHGGE DSSQESKDSG LCDFKPEPQP RHRNSLSDSA DPFLIKSPSA LLDYYQEDVS RPQPETQES SGRADKFLKP LSWGSEVLES SCNQPSTALW QLERFTVPQA LQKVRVLKHQ ELLLVVAVSS FTRHVFTCSQ S GIKVWNLV ...String:
PQFCQGFLIQ GLWELFMDSR QKNQQEHGGE DSSQESKDSG LCDFKPEPQP RHRNSLSDSA DPFLIKSPSA LLDYYQEDVS RPQPETQES SGRADKFLKP LSWGSEVLES SCNQPSTALW QLERFTVPQA LQKVRVLKHQ ELLLVVAVSS FTRHVFTCSQ S GIKVWNLV NQVAEDRDPE SHLKCSVQDN KVYLRTCLLS SNSRTLFAGG YNLPGVIVWD LAAPSLYEKC QLPCEGLSCQ AL ANTKENM ALAGFTDGTV RIWDLRTQEI VRNLKGPTNS ARNLVVKDDN IWTGGLDACL RCWDLRMAKV SLEHLFQSQI MSL AHSPTE DWLLLGLANG QHCLFNSRKR DQVLTVDTKD NTILGLKFSP NGKWWASVGM GNFITVHSMP TGAKLFQVPE VGPV RCFDM TENGRLIITG SRDCASVYHI KY

UniProtKB: Transducin-like enhancer protein 6

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Macromolecule #3: Oocyte-expressed protein homolog

MacromoleculeName: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.25276 KDa
Recombinant expressionOrganism: Spodoptera frugiperda granulovirus
SequenceString:
SLRLRTRPWW FPIQEVSNPL VLYMEAWVAE RVIGTDQAEI SEIEWMCQAL LTVDSVNSGN LAEITIFGQP SAQTRMKNIL LNMAAWHKE

UniProtKB: Oocyte-expressed protein homolog

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Macromolecule #4: Zinc finger BED domain-containing protein 3

MacromoleculeName: Zinc finger BED domain-containing protein 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 6.48345 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
SYSEAWGYFH LDPAQPRHRM MSAWATCRLC GLQVGGLPNF QMWTRALCQH LSDVHL

UniProtKB: Zinc finger BED domain-containing protein 3

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTrisTris(hydroxymethyl)aminomethane
5.0 mMDTTDithiothreitol

Details: 25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in argon atmosphere.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1993029
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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