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- PDB-8x7w: Structure of dimeric human SCMC complex -

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Basic information

Entry
Database: PDB / ID: 8x7w
TitleStructure of dimeric human SCMC complex
Components
  • Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
  • Oocyte-expressed protein homolog
  • Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
KeywordsCYTOSOLIC PROTEIN / oocyte / subcortical / complex
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / establishment of organelle localization / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / cortical granule / positive regulation of embryonic development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins ...embryonic process involved in female pregnancy / subcortical maternal complex / establishment of organelle localization / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / cortical granule / positive regulation of embryonic development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / positive regulation of meiotic nuclear division / regulation of establishment of protein localization / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / mitochondrion localization / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / establishment of spindle localization / 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 / exocytosis / replication fork processing / carbohydrate transport / ubiquitin-like protein ligase binding / regulation of cell division / protein sumoylation / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of double-strand break repair via homologous recombination / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / tubulin binding / ATP-binding cassette (ABC) transporter complex / condensed nuclear chromosome / actin filament organization / cell chemotaxis / negative regulation of canonical Wnt signaling pathway / protein tag activity / transcription corepressor 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 / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / mitochondrion / RNA binding / ATP binding / identical protein binding / nucleus / membrane / 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 / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / 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 / WD domain, G-beta repeat / 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 / 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 speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsChi, P. / Ou, G. / Liu, S. / Lu, Y. / Li, J. / Li, J. / Wang, X. / Deng, D.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
B: Oocyte-expressed protein homolog
C: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
D: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
E: Oocyte-expressed protein homolog
F: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6


Theoretical massNumber of molelcules
Total (without water)499,5456
Polymers499,5456
Non-polymers00
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 Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5


Mass: 171393.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K-12 / Gene: malE, NLRP5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P59047
#2: Protein Oocyte-expressed protein homolog


Mass: 18479.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OOEP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A6NGQ2
#3: Protein Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6


Mass: 59899.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K-12 / Gene: SMT3, TLE6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q12306, UniProt: Q9H808
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: human SCMC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 51.336 e/Å2 / Film or detector model: GATAN K2 IS (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163605 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00922888
ELECTRON MICROSCOPYf_angle_d0.74931002
ELECTRON MICROSCOPYf_dihedral_angle_d3.8683030
ELECTRON MICROSCOPYf_chiral_restr0.0393492
ELECTRON MICROSCOPYf_plane_restr0.0043932

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