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- PDB-9l4l: Structure of human SCMCcore complex contain NLRP2 -

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Basic information

Entry
Database: PDB / ID: 9l4l
TitleStructure of human SCMCcore complex contain NLRP2
Components
  • NACHT, LRR and PYD domains-containing protein 2
  • NACHT, LRR and PYD domains-containing protein 5
  • Oocyte-expressed protein homolog
  • Transducin-like enhancer protein 6
KeywordsCYTOSOLIC PROTEIN / complex
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / Pyrin domain binding / establishment of organelle localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity ...embryonic process involved in female pregnancy / subcortical maternal complex / Pyrin domain binding / establishment of organelle localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / cortical granule / positive regulation of meiotic nuclear division / positive regulation of embryonic development / regulation of establishment of protein localization / embryonic pattern specification / flagellated sperm motility / establishment of spindle localization / mitochondrion localization / epigenetic programming in the zygotic pronuclei / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of double-strand break repair / exocytosis / replication fork processing / regulation of cell division / positive regulation of double-strand break repair via homologous recombination / sperm midpiece / tubulin binding / actin filament organization / positive regulation of interleukin-1 beta production / negative regulation of canonical Wnt signaling pathway / transcription corepressor activity / regulation of protein localization / regulation of inflammatory response / cell cortex / spermatogenesis / transcription regulator complex / inflammatory response / innate immune response / intracellular membrane-bounded organelle / apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / mitochondrion / RNA binding / ATP binding / nucleus / cytoplasm / cytosol
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 / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat 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 / NACHT, LRR and PYD domains-containing protein 5 / Transducin-like enhancer protein 6 / NACHT, LRR and PYD domains-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsOu, G.J. / Liu, Q.T. / Jiao, H.Z. / Han, Z. / Li, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82401959 China
CitationJournal: To Be Published
Title: Structural assembly of the subcortical maternal complex SCMC
Authors: Ou, G.J. / Liu, Q.T.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 2
D: NACHT, LRR and PYD domains-containing protein 5
B: Oocyte-expressed protein homolog
C: Transducin-like enhancer protein 6


Theoretical massNumber of molelcules
Total (without water)335,9024
Polymers335,9024
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 NACHT, LRR and PYD domains-containing protein 2 / Nucleotide-binding site protein 1 / PYRIN domain and NACHT domain-containing protein 1 / PYRIN- ...Nucleotide-binding site protein 1 / PYRIN domain and NACHT domain-containing protein 1 / PYRIN-containing APAF1-like protein 2


Mass: 120666.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP2, NALP2, NBS1, PAN1, PYPAF2 / Production host: Homo sapiens (human) / References: UniProt: Q9NX02
#2: Protein NACHT, LRR and PYD domains-containing protein 5 / Mater protein homolog / Maternal Antigen that Embryos Require


Mass: 134499.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP5, MATER, NALP5 / Production host: Homo sapiens (human) / References: UniProt: P59047
#3: Protein Oocyte-expressed protein homolog / KH homology domain-containing protein 2 / Oocyte- and embryo-specific protein 19 / hOEP19


Mass: 17194.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OOEP, C6orf156, KHDC2, OEP19 / Production host: Homo sapiens (human) / References: UniProt: A6NGQ2
#4: Protein Transducin-like enhancer protein 6


Mass: 63541.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLE6 / Production host: Homo sapiens (human) / References: 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 SCMCcore complex contains NLRP2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 229.09 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
225 mMTris(hydroxymethyl)aminomethaneTris1
35 mMDithiothreitolDTT1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Vitrification carried out in argon atmosphere

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 1200 nm
Image recordingElectron dose: 51.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3186536 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00618568
ELECTRON MICROSCOPYf_angle_d0.79225143
ELECTRON MICROSCOPYf_dihedral_angle_d5.3562476
ELECTRON MICROSCOPYf_chiral_restr0.0392850
ELECTRON MICROSCOPYf_plane_restr0.0053210

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