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- PDB-8h93: Structure of dimeric mouse SCMC core complex -

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Basic information

Entry
Database: PDB / ID: 8h93
TitleStructure of dimeric mouse SCMC core complex
Components
  • NACHT, LRR and PYD domains-containing protein 5
  • Oocyte-expressed protein homolog
  • Transducin-like enhancer protein 6
KeywordsCYTOSOLIC PROTEIN / oocyte / subcortical / complex
Function / homology
Function and homology information


subcortical maternal complex / regulation of localization / endoplasmic reticulum localization / establishment of organelle localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / ooplasm / spermatogonial cell division / cortical granule / positive regulation of meiotic nuclear division ...subcortical maternal complex / regulation of localization / endoplasmic reticulum localization / establishment of organelle localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / ooplasm / spermatogonial cell division / cortical granule / positive regulation of meiotic nuclear division / positive regulation of embryonic development / regulation of establishment of protein localization / establishment of spindle localization / regulation of RNA stability / mitochondrion localization / apical cortex / embryonic pattern specification / fertilization / positive regulation of double-strand break repair / positive regulation of neurogenesis / replication fork processing / regulation of cell division / exocytosis / positive regulation of double-strand break repair via homologous recombination / positive regulation of neuron differentiation / embryo implantation / actin filament organization / animal organ morphogenesis / regulation of protein stability / negative regulation of canonical Wnt signaling pathway / transcription corepressor activity / protein localization / apical part of cell / regulation of protein localization / cell cortex / regulation of inflammatory response / protein-containing complex assembly / in utero embryonic development / transcription regulator complex / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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 / 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: 3.01 Å
AuthorsChi, P. / Ou, G. / Han, Z. / Li, J. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of the subcortical maternal complex and its implications in reproductive disorders.
Authors: Pengliang Chi / Guojin Ou / Dandan Qin / Zhuo Han / Jialu Li / Qingjie Xiao / Zheng Gao / Chengpeng Xu / Qianqian Qi / Qingting Liu / Sibei Liu / Jinhong Li / Li Guo / Yuechao Lu / Jing Chen ...Authors: Pengliang Chi / Guojin Ou / Dandan Qin / Zhuo Han / Jialu Li / Qingjie Xiao / Zheng Gao / Chengpeng Xu / Qianqian Qi / Qingting Liu / Sibei Liu / Jinhong Li / Li Guo / Yuechao Lu / Jing Chen / Xiang Wang / Hubing Shi / Lei Li / Dong Deng /
Abstract: The subcortical maternal complex (SCMC) plays a crucial role in early embryonic development. Malfunction of SCMC leads to reproductive diseases in women. However, the molecular function and assembly ...The subcortical maternal complex (SCMC) plays a crucial role in early embryonic development. Malfunction of SCMC leads to reproductive diseases in women. However, the molecular function and assembly basis for SCMC remain elusive. Here we reconstituted mouse SCMC and solved the structure at atomic resolution using single-particle cryo-electron microscopy. The core complex of SCMC was formed by MATER, TLE6 and FLOPED, and MATER embraced TLE6 and FLOPED via its NACHT and LRR domains. Two core complexes further dimerize through interactions between two LRR domains of MATERs in vitro. FILIA integrates into SCMC by interacting with the carboxyl-terminal region of FLOPED. Zygotes from mice with Floped C-terminus truncation showed delayed development and resembled the phenotype of zygotes from Filia knockout mice. More importantly, the assembly of mouse SCMC was affected by corresponding clinical variants associated with female reproductive diseases and corresponded with a prediction based on the mouse SCMC structure. Our study paves the way for further investigations on SCMC functions during mammalian preimplantation embryonic development and reveals underlying causes of female reproductive diseases related to SCMC mutations, providing a new strategy for the diagnosis of female reproductive disorders.
History
DepositionOct 24, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 5
B: Transducin-like enhancer protein 6
C: Oocyte-expressed protein homolog
D: NACHT, LRR and PYD domains-containing protein 5
E: Transducin-like enhancer protein 6
F: Oocyte-expressed protein homolog


Theoretical massNumber of molelcules
Total (without water)406,9776
Polymers406,9776
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 119819.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlrp5, Mater, Nalp5 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R1M5
#2: Protein Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 65187.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tle6, Grg6 / Cell line (production host): Sf9 / 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: 18481.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ooep, Oep19, Sddr / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9CWE6

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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: The mouse subcortical maternal complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197574 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322615
ELECTRON MICROSCOPYf_angle_d0.62430631
ELECTRON MICROSCOPYf_dihedral_angle_d4.442970
ELECTRON MICROSCOPYf_chiral_restr0.043528
ELECTRON MICROSCOPYf_plane_restr0.0053876

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