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- PDB-9ln6: Structure of human NLRP14-UHRF1 complex -

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Basic information

Entry
Database: PDB / ID: 9ln6
TitleStructure of human NLRP14-UHRF1 complex
Components
  • Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1
  • Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14
KeywordsCYTOSOLIC PROTEIN / maternal complex / UHRF1 / NLRP14 / ubiquitylation
Function / homology
Function and homology information


histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / histone H3K23 ubiquitin ligase activity / DNA damage sensor activity / chromosomal DNA methylation maintenance following DNA replication / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding ...histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / histone H3K23 ubiquitin ligase activity / DNA damage sensor activity / chromosomal DNA methylation maintenance following DNA replication / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / detection of maltose stimulus / maltose transport complex / carbohydrate transport / positive regulation of protein metabolic process / mitotic spindle assembly / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / heterochromatin / protein localization to chromatin / epigenetic regulation of gene expression / ATP-binding cassette (ABC) transporter complex / DNA methylation / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / cell chemotaxis / euchromatin / RING-type E3 ubiquitin transferase / double-strand break repair via homologous recombination / spindle / nuclear matrix / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / outer membrane-bounded periplasmic space / regulation of inflammatory response / histone binding / spermatogenesis / nucleic acid binding / ubiquitin-dependent protein catabolic process / cell differentiation / periplasmic space / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : / 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 / PUA-like 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 / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Zinc finger PHD-type signature. / Ring finger / 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-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / NACHT, LRR and PYD domains-containing protein 14 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsQi, Q. / Chi, P. / Liu, S. / Lu, Y. / Li, J. / Li, J. / Wang, X. / Jiang, Y. / Deng, D.
Funding support China, 1items
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
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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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 14
B: Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)225,5132
Polymers225,5132
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 14 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nucleotide-binding ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nucleotide-binding oligomerization domain protein 5


Mass: 170249.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, NLRP14, NALP14, NOD5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0AEX9, UniProt: Q86W24
#2: Protein Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Inverted CCAAT box-binding ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / HuNp95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 55263.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, UHRF1, ICBP90, NP95, RNF106 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0AEX9, UniProt: Q96T88, RING-type E3 ubiquitin transferase
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: binary complex of NLRP14 and UHRF1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 1.7 mg/ml / Embedding 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: 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: 55.13 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73160 / Symmetry type: POINT
RefinementHighest resolution: 3.49 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058287
ELECTRON MICROSCOPYf_angle_d0.59511189
ELECTRON MICROSCOPYf_dihedral_angle_d10.8753100
ELECTRON MICROSCOPYf_chiral_restr0.0391272
ELECTRON MICROSCOPYf_plane_restr0.0041421

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