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- EMDB-34552: Structure of dimeric mouse SCMC core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34552
TitleStructure of dimeric mouse SCMC core complex
Map data
Sample
  • Complex: The mouse subcortical maternal complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog
Keywordsoocyte / subcortical / complex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


subcortical maternal complex / establishment of organelle localization / regulation of localization / endoplasmic reticulum localization / embryonic process involved in female pregnancy / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / ooplasm / spermatogonial cell division / positive regulation of meiotic nuclear division ...subcortical maternal complex / establishment of organelle localization / regulation of localization / endoplasmic reticulum localization / embryonic process involved in female pregnancy / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / ooplasm / spermatogonial cell division / positive regulation of meiotic nuclear division / cortical granule / positive regulation of embryonic development / regulation of establishment of protein localization / regulation of RNA stability / establishment of spindle localization / mitochondrion localization / apical cortex / embryonic pattern specification / fertilization / positive regulation of double-strand break repair / positive regulation of neurogenesis / positive regulation of double-strand break repair via homologous recombination / replication fork processing / regulation of cell division / exocytosis / embryo implantation / positive regulation of neuron differentiation / tubulin binding / actin filament organization / animal organ morphogenesis / regulation of protein stability / negative regulation of canonical Wnt signaling pathway / protein localization / transcription corepressor activity / regulation of protein localization / apical part of cell / cell cortex / regulation of inflammatory response / protein-containing complex assembly / in utero embryonic development / transcription regulator complex / intracellular membrane-bounded organelle / 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 / NACHT domain / NACHT-NTPase domain profile. ...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. / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChi P / Ou G / Han Z / Li J / Deng D
Funding support China, 1 items
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, 2022-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34552.png

Downloads & links

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Map

FileDownload / File: emd_34552.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.256
Minimum - Maximum-1.5000986 - 2.9744112
Average (Standard dev.)0.0003659482 (±0.045800574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34552_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_34552_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The mouse subcortical maternal complex

EntireName: The mouse subcortical maternal complex
Components
  • Complex: The mouse subcortical maternal complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog

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Supramolecule #1: The mouse subcortical maternal complex

SupramoleculeName: The mouse subcortical maternal complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 119.819859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGPPEKDSKA ILKARGLEEE QKSESTMSPS ENVSRAILKD SGSEEVEQAS ERKMTSPEND SKSIQKDQGP EQEQTSETLQ SKEEDEVTE ADKDNGGDLQ DYKAHVIAKF DTSVDLHYDS PEMKLLSDAF KPYQKTFQPH TIILHGRPGV GKSALARSIV L GWAQGKLF ...String:
MGPPEKDSKA ILKARGLEEE QKSESTMSPS ENVSRAILKD SGSEEVEQAS ERKMTSPEND SKSIQKDQGP EQEQTSETLQ SKEEDEVTE ADKDNGGDLQ DYKAHVIAKF DTSVDLHYDS PEMKLLSDAF KPYQKTFQPH TIILHGRPGV GKSALARSIV L GWAQGKLF QKMSFVIFFS VREIKWTEKS SLAQLIAKEC PDSWDLVTKI MSQPERLLFV IDGLDDMDSV LQHDDMTLSR DW KDEQPIY ILMYSLLRKA LLPQSFLIIT TRNTGLEKLK SMVVSPLYIL VEGLSASRRS QLVLENISNE SDRIQVFHSL IEN HQLFDQ CQAPSVCSLV CEALQLQKKL GKRCTLPCQT LTGLYATLVF HQLTLKRPSQ SALSQEEQIT LVGLCMMAAE GVWT MRSVF YDDDLKNYSL KESEILALFH MNILLQVGHN SEQCYVFSHL SLQDFFAALY YVLEGLEEWN QHFCFIENQR SIMEV KRTD DTRLLGMKRF LFGLMNKDIL KTLEVLFEYP VIPTVEQKLQ HWVSLIAQQV NGTSPMDTLD AFYCLFESQD EEFVGG ALK RFQEVWLLIN QKMDLKVSSY CLKHCQNLKA IRVDIRDLLS VDNTLELCPV VTVQETQCKP LLMEWWGNFC SVLGSLR NL KELDLGDSIL SQRAMKILCL ELRNQSCRIQ KLTFKSAEVV SGLKHLWKLL FSNQNLKYLN LGNTPMKDDD MKLACEAL K HPKCSVETLR LDSCELTIIG YEMISTLLIS TTRLKCLSLA KNRVGVKSMI SLGNALSSSM CLLQKLILDN CGLTPASCH LLVSALFSNQ NLTHLCLSNN SLGTEGVQQL CQFLRNPECA LQRLILNHCN IVDDAYGFLA MRLANNTKLT HLSLTMNPVG DGAMKLLCE ALKEPTCYLQ ELELVDCQLT QNCCEDLACM ITTTKHLKSL DLGNNALGDK GVITLCEGLK QSSSSLRRLG L GACKLTSN CCEALSLAIS CNPHLNSLNL VKNDFSTSGM LKLCSAFQCP VSNLGIIGLW KQEYYARVRR QLEEVEFVKP HV VIDGDWY ASDEDDRNWW KN

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.187332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTSHRQSSDT FGGILPSTLS SRYLSIVNQL PEEFSSVVSE MMVHLENIFS LAENFFQAIE RFSRTPDLLE RNKMSIGVGA EGDSWPCHV SHEAPMGSAQ TTENSAKEED KQVPESAALQ HPKFKSTPGP QLPTRRRFLS ESDELQDPQP VWDAEPQFCQ G FLIQGLWE ...String:
MTSHRQSSDT FGGILPSTLS SRYLSIVNQL PEEFSSVVSE MMVHLENIFS LAENFFQAIE RFSRTPDLLE RNKMSIGVGA EGDSWPCHV SHEAPMGSAQ TTENSAKEED KQVPESAALQ HPKFKSTPGP QLPTRRRFLS ESDELQDPQP VWDAEPQFCQ G FLIQGLWE LFMDSRQKNQ QEHGGEDSSQ ESKDSGLCDF KPEPQPRHRN SLSDSADPFL IKSPSALLDY YQEDVSRPQP ET QESSGRA DKFLKPLSWG SEVLESSCNQ PSTALWQLER FTVPQALQKV RVLKHQELLL VVAVSSFTRH VFTCSQSGIK VWN LVNQVA EDRDPESHLK CSVQDNKVYL RTCLLSSNSR TLFAGGYNLP GVIVWDLAAP SLYEKCQLPC EGLSCQALAN TKEN MALAG FTDGTVRIWD LRTQEIVRNL KGPTNSARNL VVKDDNIWTG GLDACLRCWD LRMAKVSLEH LFQSQIMSLA HSPTE DWLL LGLANGQHCL FNSRKRDQVL TVDTKDNTIL GLKFSPNGKW WASVGMGNFI TVHSMPTGAK LFQVPEVGPV RCFDMT ENG RLIITGSRDC ASVYHIKY

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.481295 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASHTADADA KPDSDSQKLL NVLPVSLRLR TRPWWFPIQE VSNPLVLYME AWVAERVIGT DQAEISEIEW MCQALLTVDS VNSGNLAEI TIFGQPSAQT RMKNILLNMA AWHKENELQR AVKVKEVEEF LKIRASSILS KLSKKGLKLA GFPLPLEGRE T QMES

UniProtKB: Oocyte-expressed protein homolog

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.1 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 197574

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