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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 H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / : / methyl-CpG binding / histone H3K9me2/3 reader activity / detection of maltose stimulus / negative regulation of gene expression via chromosomal CpG island methylation ...histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / : / methyl-CpG binding / histone H3K9me2/3 reader activity / detection of maltose stimulus / negative regulation of gene expression via chromosomal CpG island methylation / maltose transport complex / carbohydrate transport / positive regulation of protein metabolic process / carbohydrate transmembrane transporter activity / maltose binding / mitotic spindle assembly / 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 / ATP-binding cassette (ABC) transporter complex / epigenetic regulation of gene expression / replication fork / DNA methylation / 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 / ubiquitin-dependent protein catabolic process / nucleic acid binding / 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 / Bacterial extracellular solute-binding protein / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 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: To Be Published
Title: Structure of human NLRP14-UHRF1 complex
Authors: Qi Q / Chi P / Liu S / Lu Y / Li J / Li J / Wang X / Jiang Y / Deng D
History
DepositionJan 20, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 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

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63227_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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