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- EMDB-38128: Structure of human SCMC ternary complex -

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Entry
Database: EMDB / ID: EMD-38128
TitleStructure of human SCMC ternary complex
Map data
Sample
  • Complex: human SCMC ternary complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
Keywordsoocyte / subcortical / complex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / regulation of localization / endoplasmic reticulum localization / establishment of organelle localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / SUMO is conjugated to E1 (UBA2:SAE1) / cortical granule / SUMOylation of nuclear envelope proteins ...embryonic process involved in female pregnancy / subcortical maternal complex / regulation of localization / endoplasmic reticulum localization / establishment of organelle localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / SUMO is conjugated to E1 (UBA2:SAE1) / cortical granule / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / positive regulation of meiotic nuclear division / positive regulation of embryonic development / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / regulation of establishment of protein localization / establishment of spindle localization / septin ring / mitochondrion localization / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / embryonic pattern specification / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / positive regulation of double-strand break repair / detection of maltose stimulus / maltose transport complex / replication fork processing / ubiquitin-like protein ligase binding / regulation of cell division / maltose binding / carbohydrate transport / exocytosis / maltose transport / maltodextrin transmembrane transport / protein sumoylation / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of double-strand break repair via homologous recombination / tubulin binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / condensed nuclear chromosome / actin filament organization / negative regulation of canonical Wnt signaling pathway / transcription corepressor activity / protein tag activity / regulation of protein localization / outer membrane-bounded periplasmic space / cell cortex / regulation of inflammatory response / transcription regulator complex / periplasmic space / intracellular membrane-bounded organelle / DNA damage response / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / RNA binding / ATP binding / identical protein binding / membrane / 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 / DAPIN domain ...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 / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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 / Maltose/maltodextrin-binding periplasmic protein / NACHT, LRR and PYD domains-containing protein 5 / Ubiquitin-like protein SMT3 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChi P / Ou G / Liu S / Lu Y / Li JH / Li JL / Wang X / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171211 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cryo-EM structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants.
Authors: Pengliang Chi / Guojin Ou / Sibei Liu / Qianhong Ma / Yuechao Lu / Jinhong Li / Jialu Li / Qianqian Qi / Zhuo Han / Zihan Zhang / Qingting Liu / Li Guo / Jing Chen / Xiang Wang / Wei Huang / ...Authors: Pengliang Chi / Guojin Ou / Sibei Liu / Qianhong Ma / Yuechao Lu / Jinhong Li / Jialu Li / Qianqian Qi / Zhuo Han / Zihan Zhang / Qingting Liu / Li Guo / Jing Chen / Xiang Wang / Wei Huang / Lei Li / Dong Deng /
Abstract: The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, ...The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants.
History
DepositionNov 26, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38128.png

Downloads & links

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Map

FileDownload / File: emd_38128.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.2158194 - 1.7158313
Average (Standard dev.)-0.00014587509 (±0.034783673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38128_msk_1.map
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Half map: #2

Fileemd_38128_half_map_1.map
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Half map: #1

Fileemd_38128_half_map_2.map
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Sample components

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Entire : human SCMC ternary complex

EntireName: human SCMC ternary complex
Components
  • Complex: human SCMC ternary complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6

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Supramolecule #1: human SCMC ternary complex

SupramoleculeName: human SCMC ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and P...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 171.393734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKGS MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE L KAKGKSAL ...String:
MDYKDDDDKG DYKDDDDKGS MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE L KAKGKSAL MFNLQEPYFT WPLIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NK GETAMTI NGPWAWSNID TSKVNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPL GAVALK SYEEELAKDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TLTFSSYGLQ WCLY ELDKE EFQTFKELLK KKSSESTTCS IPQFEIENAN VECLALLLHE YYGASLAWAT SISIFENMNL RTLSEKARDD MKRHS PEDP EATMTDQGPS KEKVPGISQA VQQDSATAAE TKEQEISQAM EQEGATAAET EEQEISQAME QEGATAAETE EQGHGG DTW DYKSHVMTKF AEEEDVRRSF ENTAADWPEM QTLAGAFDSD RWGFRPRTVV LHGKSGIGKS ALARRIVLCW AQGGLYQ GM FSYVFFLPVR EMQRKKESSV TEFISREWPD SQAPVTEIMS RPERLLFIID GFDDLGSVLN NDTKLCKDWA EKQPPFTL I RSLLRKVLLP ESFLIVTVRD VGTEKLKSEV VSPRYLLVRG ISGEQRIHLL LERGIGEHQK TQGLRAIMNN RELLDQCQV PAVGSLICVA LQLQDVVGES VAPFNQTLTG LHAAFVFHQL TPRGVVRRCL NLEERVVLKR FCRMAVEGVW NRKSVFDGDD LMVQGLGES ELRALFHMNI LLPDSHCEEY YTFFHLSLQD FCAALYYVLE GLEIEPALCP LYVEKTKRSM ELKQAGFHIH S LWMKRFLF GLVSEDVRRP LEVLLGCPVP LGVKQKLLHW VSLLGQQPNA TTPGDTLDAF HCLFETQDKE FVRLALNSFQ EV WLPINQN LDLIASSFCL QHCPYLRKIR VDVKGIFPRD ESAEACPVVP LWMRDKTLIE EQWEDFCSML GTHPHLRQLD LGS SILTER AMKTLCAKLR HPTCKIQTLM FRNAQITPGV QHLWRIVMAN RNLRSLNLGG THLKEEDVRM ACEALKHPKC LLES LRLDC CGLTHACYLK ISQILTTSPS LKSLSLAGNK VTDQGVMPLS DALRVSQCAL QKLILEDCGI TATGCQSLAS ALVSN RSLT HLCLSNNSLG NEGVNLLCRS MRLPHCSLQR LMLNQCHLDT AGCGFLALAL MGNSWLTHLS LSMNPVEDNG VKLLCE VMR EPSCHLQDLE LVKCHLTAAC CESLSCVISR SRHLKSLDLT DNALGDGGVA ALCEGLKQKN SVLARLGLKA CGLTSDC CE ALSLALSCNR HLTSLNLVQN NFSPKGMMKL CSAFACPTSN LQIIGLWKWQ YPVQIRKLLE EVQLLKPRVV IDGSWHSF D EDDRYWWKN

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, NACHT, LRR and PYD domains-containing protein 5

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Macromolecule #2: Oocyte-expressed protein homolog

MacromoleculeName: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.479176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVDDAGAAES QRGKQTPAHS LEQLRRLPLP PPQIRIRPWW FPVQELRDPL VFYLEAWLAD ELFGPDRAII PEMEWTSQAL LTVDIVDSG NLVEITVFGR PRVQNRVKSM LLCLAWFHRE HRARAEKMKH LEKNLKAHAS DPHSPQDPVA LEWSHPQFEK

UniProtKB: Oocyte-expressed protein homolog

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Macromolecule #3: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6

MacromoleculeName: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.899367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG TMSDSEVNQE AKPEVKPEVK PETHINLKVS DGSSEIFFKI KKTTPLRRLM EAFAKRQGKE MDSLRFLYDG IRIQADQTP EDLDMEDNDI IEAHREQIGG LFWDKEPWFW HDTLTEQLWR IFAGVHDEKA KPRDRQQAPG LGQESKAPGS C DPGTDPCP ...String:
MWSHPQFEKG TMSDSEVNQE AKPEVKPEVK PETHINLKVS DGSSEIFFKI KKTTPLRRLM EAFAKRQGKE MDSLRFLYDG IRIQADQTP EDLDMEDNDI IEAHREQIGG LFWDKEPWFW HDTLTEQLWR IFAGVHDEKA KPRDRQQAPG LGQESKAPGS C DPGTDPCP EDASTPRPPE ASSSPPEGSQ DRNTSWGVVQ EPPGRASRFL QSISWDPEDF EDAWKRPDAL PGQSKRLAVP CK LEKMRIL AHGELVLATA ISSFTRHVFT CGRRGIKVWS LTGQVAEDRF PESHLPIQTP GAFLRTCLLS SNSRSLLTGG YNL ASVSVW DLAAPSLHVK EQLPCAGLNC QALDANLDAN LAFASFTSGV VRIWDLRDQS VVRDLKGYPD GVKSIVVKGY NIWT GGPDA CLRCWDQRTI MKPLEYQFKS QIMSLSHSPQ EDWVLLGMAN GQQWLQSTSG SQRHMVGQKD SVILSVKFSP FGQWW ASVG MDDFLGVYSM PAGTKVFEVP EMSPVTCCDV SSNNRLVVTG SGEHASVYQI TY

UniProtKB: Ubiquitin-like protein SMT3, Transducin-like enhancer protein 6

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.336 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: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280159
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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