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- EMDB-66415: Structure of dimeric mouse NLRP14-KDM2A-SKP1 complex /Focused Map A -

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Basic information

Entry
Database: EMDB / ID: EMD-66415
TitleStructure of dimeric mouse NLRP14-KDM2A-SKP1 complex /Focused Map A
Map data
Sample
  • Complex: Dimeric mouse NLRP14-KDM2A-SKP1 complex
KeywordsCryo-EM / NLRP14 / KDM2A / SKP1 / early embryonic development / CYTOSOLIC PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsLiu S / Jiao H / Yan L / Qi Q / Chi P / Lu Y / Li JH / Li JL / Ju S / Wang X ...Liu S / Jiao H / Yan L / Qi Q / Chi P / Lu Y / Li JH / Li JL / Ju S / Wang X / Hu H / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: Nat Commun / Year: 2026
Title: NLRP14 modulates the activity of E3 ubiquitin ligases during the oocyte-to-embryo transition.
Authors: Sibei Liu / Qianqian Qi / Pengliang Chi / Haizhan Jiao / Li Yan / Yuechao Lu / Rongrong Zhang / Jinhong Li / Sicheng Ju / Zhuo Han / Zihan Zhang / Qingting Liu / Guojin Ou / Jialu Li / Jing ...Authors: Sibei Liu / Qianqian Qi / Pengliang Chi / Haizhan Jiao / Li Yan / Yuechao Lu / Rongrong Zhang / Jinhong Li / Sicheng Ju / Zhuo Han / Zihan Zhang / Qingting Liu / Guojin Ou / Jialu Li / Jing Chen / Xiang Wang / Lei Li / Li Guo / Xue Jiao / Hongli Hu / Yongmei Jiang / Dong Deng /
Abstract: NLRP14 is an essential maternal factor for mammalian embryonic development. Maternal ablation of NLRP14 in mice impairs DNA demethylation and calcium homeostasis in zygotes, causing early embryonic ...NLRP14 is an essential maternal factor for mammalian embryonic development. Maternal ablation of NLRP14 in mice impairs DNA demethylation and calcium homeostasis in zygotes, causing early embryonic arrest. However, the underlying biochemical events remain largely unknown. Here, we identified two binding partners (KDM2A and UHRF1) of NLRP14 and further solved structures of NLRP14-KDM2A-SKP1 and NLRP14-UHRF1. Structural analysis revealed that NLRP14 modulates the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase and the RING-type E3 ubiquitin ligase UHRF1 through two distinct mechanisms. Mechanistically, NLRP14 competitively inhibits KDM2A-mediated SCF assembly or allosterically inhibits the activity of UHRF1 by occupying the E2 ubiquitin-conjugating enzyme (UBE2D) binding site of the ubiquitin-like (UBL) domain. Deletion of NLRP14 in mice increases ubiquitination levels in oocytes during maturation and after fertilization. Collectively, our findings identify NLRP14 as a dual regulator that restrains E3 ubiquitin ligase-driven ubiquitination by limiting SCF complex assembly and attenuating UHRF1 activity. This regulatory role is required to prevent excessive protein ubiquitination and maintain proteostasis during the oocyte-to-embryo transition, thereby supporting early embryonic development. Our study uncovers maternal regulation of proteostasis in oocytes and suggests that dysregulating proteostasis is an important factor in the pathogenesis of reproductive disorders.
History
DepositionSep 29, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66415.png

Downloads & links

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Map

FileDownload / File: emd_66415.map.gz / Format: CCP4 / Size: 178 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.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.24130532 - 0.5102527
Average (Standard dev.)0.00041297605 (±0.014332111)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66415_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_66415_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Dimeric mouse NLRP14-KDM2A-SKP1 complex

EntireName: Dimeric mouse NLRP14-KDM2A-SKP1 complex
Components
  • Complex: Dimeric mouse NLRP14-KDM2A-SKP1 complex

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Supramolecule #1: Dimeric mouse NLRP14-KDM2A-SKP1 complex

SupramoleculeName: Dimeric mouse NLRP14-KDM2A-SKP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.633 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49652
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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