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- PDB-9wsr: Structure of mouse NLRP14-KDM2A-SKP1 complex -

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Basic information

Entry
Database: PDB / ID: 9wsr
TitleStructure of mouse NLRP14-KDM2A-SKP1 complex
Components
  • Lysine-specific demethylase 2A
  • NACHT, LRR and PYD domains-containing protein 14
  • S-phase kinase-associated protein 1
KeywordsCYTOSOLIC PROTEIN / Cryo-EM / Complex / early embryonic development / NLRP14 / KDM2A / SKP1 / ubiquitylation.
Function / homology
Function and homology information


Prolactin receptor signaling / SCF-beta-TrCP mediated degradation of Emi1 / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / HDMs demethylate histones / Regulation of BACH1 activity / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / SCF(Skp2)-mediated degradation of p27/p21 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Regulation of RUNX2 expression and activity ...Prolactin receptor signaling / SCF-beta-TrCP mediated degradation of Emi1 / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / HDMs demethylate histones / Regulation of BACH1 activity / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / SCF(Skp2)-mediated degradation of p27/p21 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Degradation of beta-catenin by the destruction complex / Iron uptake and transport / Activation of NF-kappaB in B cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / F-box domain binding / neuroepithelial cell differentiation / GLI3 is processed to GLI3R by the proteasome / histone H3K36 demethylase activity / Regulation of PLK1 Activity at G2/M Transition / PcG protein complex / unmethylated CpG binding / Neddylation / : / gap junction / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of epithelial cell apoptotic process / ubiquitin ligase activator activity / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / heart looping / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / protein K48-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / transcription initiation-coupled chromatin remodeling / molecular function activator activity / circadian regulation of gene expression / neural tube closure / regulation of circadian rhythm / beta-catenin binding / multicellular organism growth / neuron differentiation / protein polyubiquitination / regulation of inflammatory response / spermatogenesis / ubiquitin-dependent protein catabolic process / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / chromatin remodeling / protein domain specific binding / negative regulation of gene expression / apoptotic process / positive regulation of gene expression / centrosome / negative regulation of apoptotic process / chromatin / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain ...PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / NACHT nucleoside triphosphatase / NACHT domain / F-box-like / NACHT-NTPase domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / SKP1/BTB/POZ domain superfamily / Zinc finger PHD-type profile. / Leucine-rich repeat / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lysine-specific demethylase 2A / NACHT, LRR and PYD domains-containing protein 14 / S-phase kinase-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLiu, S. / Jiao, H. / Yan, L. / Qi, Q. / Chi, P. / Lu, Y. / Li, J.H. / Li, J.L. / Ju, S. / Wang, X. ...Liu, S. / Jiao, H. / Yan, L. / Qi, Q. / Chi, P. / Lu, Y. / Li, J.H. / Li, J.L. / Ju, S. / Wang, X. / Hu, H. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: To Be Published
Title: NLRP14 modulates the activity of E3 ubiquitin ligases during the oocyte-to-embryo transition
Authors: Liu, S. / Jiao, H. / Yan, L.
History
DepositionSep 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
B: Lysine-specific demethylase 2A
C: S-phase kinase-associated protein 1
A: NACHT, LRR and PYD domains-containing protein 14


Theoretical massNumber of molelcules
Total (without water)176,5063
Polymers176,5063
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 Lysine-specific demethylase 2A / F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing ...F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 40626.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: KDM2A fused Strep tag at the N-terminal / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbl11, Fbxl11, Jhdm1a, Kiaa1004 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P59997, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / S-phase kinase-associated protein 1A / p19A / p19skp1


Mass: 20025.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SKP1 fused Strep tag at the N-terminal / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Skp1, Skp1a / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9WTX5
#3: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 115853.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NLRP14 fused Flag tag at the N-terminal / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlrp14, Nalp14 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q6B966
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: NLRP14-KDM2A-SKP1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
125 mMTris1
2150 mMNaCl1
32 mMDTT1
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 55.225 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293321 / Symmetry type: POINT
RefinementCross valid method: NONE

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