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- PDB-9l4k: Structure of human NLRP2-TLE6-OOEP complex -

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Basic information

Entry
Database: PDB / ID: 9l4k
TitleStructure of human NLRP2-TLE6-OOEP complex
Components
  • NACHT, LRR and PYD domains-containing protein 2
  • Oocyte-expressed protein homolog
  • Transducin-like enhancer protein 6
KeywordsCYTOSOLIC PROTEIN / complex
Function / homology
Function and homology information


subcortical maternal complex / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / embryonic process involved in female pregnancy / endoplasmic reticulum localization / Pyrin domain binding / establishment or maintenance of apical/basal cell polarity / positive regulation of meiotic nuclear division / positive regulation of embryonic development ...subcortical maternal complex / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / embryonic process involved in female pregnancy / endoplasmic reticulum localization / Pyrin domain binding / establishment or maintenance of apical/basal cell polarity / positive regulation of meiotic nuclear division / positive regulation of embryonic development / regulation of establishment of protein localization / embryonic pattern specification / mitochondrion localization / establishment of spindle localization / flagellated sperm motility / negative regulation of non-canonical NF-kappaB signal transduction / epigenetic programming in the zygotic pronuclei / positive regulation of double-strand break repair / replication fork processing / regulation of cell division / positive regulation of double-strand break repair via homologous recombination / positive regulation of interleukin-1 beta production / actin filament organization / negative regulation of canonical Wnt signaling pathway / transcription corepressor activity / regulation of protein localization / regulation of inflammatory response / sperm midpiece / cell cortex / spermatogenesis / transcription regulator complex / inflammatory response / innate immune response / apoptotic process / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / 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 / 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. / DAPIN domain profile. / DAPIN domain / 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 / 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: 3.41 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: Structure / Year: 2026
Title: Structural assembly of the subcortical maternal complex SCMC.
Authors: Guojin Ou / Qingting Liu / Haizhan Jiao / Zhuo Han / Jinhong Li / Ling Min / Pengliang Chi / Sibei Liu / Jialu Li / Qianqian Qi / Zihan Zhang / Li Guo / Xiang Wang / Lei Li / Jing Chen / Hongli Hu / Dong Deng /
Abstract: The subcortical maternal complex (SCMC) is essential for mammalian preimplantation development, yet how SCMC (MATER/NLRP5, TLE6, FLOPED/OOEP) engages regulatory partners remains unclear. We ...The subcortical maternal complex (SCMC) is essential for mammalian preimplantation development, yet how SCMC (MATER/NLRP5, TLE6, FLOPED/OOEP) engages regulatory partners remains unclear. We determined cryo-EM structures of mouse SCMC bound to ZBED3 and human SCMC bound to NLRP2. Our structure reveals that ZBED3 interacts with all three SCMC subunits via its zinc finger domain, with conserved residue Phe73 mediating specific contacts. In contrast, human NLRP2 only binds to the WD40 domain of TLE6 through its leucine-rich repeat (LRR) domain. Similar interactions were also confirmed for NLRP7 with TLE6. These findings were cross-validated by in vivo proximity ligation and in vitro pull-down assays. Our work proposes a paradigmatic "Lego-like" assembly model, where the SCMC sequentially recruits different partners through diverse molecular interfaces. These findings provide critical structural insights into the SCMC's architecture and its multifaceted regulatory roles in early mammalian embryogenesis.
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
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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
Revision 1.1Apr 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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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 2
B: Transducin-like enhancer protein 6
C: Oocyte-expressed protein homolog


Theoretical massNumber of molelcules
Total (without water)201,4023
Polymers201,4023
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 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
#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
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: Structure of human NLRP2-TLE6-OOEP 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: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 1100 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 / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1347512 / Symmetry type: POINT
RefinementHighest resolution: 3.41 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210061
ELECTRON MICROSCOPYf_angle_d0.51513637
ELECTRON MICROSCOPYf_dihedral_angle_d12.5593703
ELECTRON MICROSCOPYf_chiral_restr0.0391554
ELECTRON MICROSCOPYf_plane_restr0.0041745

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