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- EMDB-63227: Structure of human NLRP14-UHRF1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63227
TitleStructure of human NLRP14-UHRF1 complex
Map data
Sample
  • Complex: binary complex of NLRP14 and UHRF1
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1
Keywordsmaternal complex / UHRF1 / NLRP14 / ubiquitylation / CYTOSOLIC PROTEIN
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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsQi Q / Chi P / Liu S / Lu Y / Li J / Wang X / Jiang Y / 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
DepositionJan 20, 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_63227.png

Downloads & links

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Map

FileDownload / File: emd_63227.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.072
Minimum - Maximum-0.46399733 - 0.9115612
Average (Standard dev.)-0.0001105408 (±0.016554918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63227_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_63227_half_map_2.map
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Sample components

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Entire : binary complex of NLRP14 and UHRF1

EntireName: binary complex of NLRP14 and UHRF1
Components
  • Complex: binary complex of NLRP14 and UHRF1
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1

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Supramolecule #1: binary complex of NLRP14 and UHRF1

SupramoleculeName: binary complex of NLRP14 and UHRF1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and P...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170.249406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKD EVDAGSGHMK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGY AQSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK A KGKSALMF ...String:
MWSHPQFEKD EVDAGSGHMK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGY AQSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK A KGKSALMF NLQEPYFTWP LIAADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLVDLI KNKHMNADTD YSIAEAAFNK GE TAMTING PWAWSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGA VALKSY EEELAKDPRI AATMENAQKG EIMPNIPQMS AFWYAVRTAV INAASGRQTV DEALKDAQTN SSSNNNNNNN NNNL GIDLE VLFQGPGTMA DSSSSSFFPD FGLLLYLEEL NKEELNTFKL FLKETMEPEH GLTPWNEVKK ARREDLANLM KKYYP GEKA WSVSLKIFGK MNLKDLCERA KEEINWSAQT IGPDDAKAGE TQEDQEAVLG DGTEYRNRIK EKFCITWDKK SLAGKP EDF HHGIAEKDRK LLEHLFDVDV KTGAQPQIVV LQGAAGVGKT TLVRKAMLDW AEGSLYQQRF KYVFYLNGRE INQLKER SF AQLISKDWPS TEGPIEEIMY QPSSLLFIID SFDELNFAFE EPEFALCEDW TQEHPVSFLM SSLLRKVMLP EASLLVTT R LTTSKRLKQL LKNHHYVELL GMSEDAREEY IYQFFEDKRW AMKVFSSLKS NEMLFSMCQV PLVCWAACTC LKQQMEKGG DVTLTCQTTT ALFTCYISSL FTPVDGGSPS LPNQAQLRRL CQVAAKGIWT MTYVFYRENL RRLGLTQSDV SSFMDSNIIQ KDAEYENCY VFTHLHVQEF FAAMFYMLKG SWEAGNPSCQ PFEDLKSLLQ STSYKDPHLT QMKCFLFGLL NEDRVKQLER T FNCKMSLK IKSKLLQCME VLGNSDYSPS QLGFLELFHC LYETQDKAFI SQAMRCFPKV AINICEKIHL LVSSFCLKHC RC LRTIRLS VTVVFEKKIL KTSLPTNTWD GDRITHCWQD LCSVLHTNEH LRELDLYHSN LDKSAMNILH HELRHPNCKL QKL LLKFIT FPDGCQDIST SLIHNKNLMH LDLKGSDIGD NGVKSLCEAL KHPECKLQTL RLESCNLTVF CCLNISNALI RSQS LIFLN LSTNNLLDDG VQLLCEALRH PKCYLERLSL ESCGLTEAGC EYLSLALISN KRLTHLCLAD NVLGDGGVKL MSDAL QHAQ CTLKSLVLRR CHFTSLSSEY LSTSLLHNKS LTHLDLGSNW LQDNGVKLLC DVFRHPSCNL QDLELMGCVL TNACCL DLA SVILNNPNLR SLDLGNNDLQ DDGVKILCDA LRYPNCNIQR LGLEYCGLTS LCCQDLSSAL ICNKRLIKMN LTQNTLG YE GIVKLYKVLK SPKCKLQVLG LCKEAFDEEA QKLLEAVGVS NPHLIIKPDC NYHNEEDVSW WWCF

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, NACHT, LRR and PYD domains-containing protein 14

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-pro...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.263094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HSGDEVDAGS GHMKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDR FGGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD K ELKAKGKS ...String:
MHHHHHHHHH HSGDEVDAGS GHMKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDR FGGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD K ELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AF NKGETAM TINGPWAWSN IDTSKVNYGV TVLPTFKGQP SKPFVGVLSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDK PLGAVA LKSYEEELAK DPRIAATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTVDEALKD AQTNSSSNNN NNNN NNNLG IDLEVLFQGP GTMWIQVRTM DGRQTHTVDS LSRLTKVEEL RRKIQELFHV EPGLQRLFYR GKQMEDGHTL FDYEV RLND TIQLLVRQSL V

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, E3 ubiquitin-protein ligase UHRF1

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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

Concentration1.7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.13 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73160
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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