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- EMDB-62814: Structure of human NLRP2-TLE6-OOEP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62814
TitleStructure of human NLRP2-TLE6-OOEP complex
Map data
Sample
  • Complex: Structure of human NLRP2-TLE6-OOEP complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 2
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog
Keywordscomplex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / Pyrin domain binding / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / positive regulation of meiotic nuclear division / positive regulation of embryonic development ...embryonic process involved in female pregnancy / subcortical maternal complex / Pyrin domain binding / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / positive regulation of meiotic nuclear division / positive regulation of embryonic development / regulation of establishment of protein localization / embryonic pattern specification / flagellated sperm motility / establishment of spindle localization / mitochondrion localization / epigenetic programming in the zygotic pronuclei / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of double-strand break repair / replication fork processing / regulation of cell division / positive regulation of double-strand break repair via homologous recombination / sperm midpiece / actin filament organization / positive regulation of interleukin-1 beta production / negative regulation of canonical Wnt signaling pathway / transcription corepressor activity / regulation of protein localization / regulation of inflammatory response / cell cortex / spermatogenesis / transcription regulator complex / inflammatory response / innate immune response / intracellular membrane-bounded organelle / apoptotic process / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / RNA binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain ...KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / WD domain, G-beta repeat / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Oocyte-expressed protein homolog / Transducin-like enhancer protein 6 / NACHT, LRR and PYD domains-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsOu GJ / Liu QT / Jiao HZ / Han Z / Li JH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82401959 China
CitationJournal: To Be Published
Title: A Versatile Recognition and Assembly Model for the subcortical maternal complex SCMC
Authors: Ou GJ / Liu QT
History
DepositionDec 20, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62814.png

Downloads & links

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Map

FileDownload / File: emd_62814.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. 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: 0.113
Minimum - Maximum-0.92839694 - 1.629073
Average (Standard dev.)0.000044572174 (±0.020109965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62814_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62814_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 : Structure of human NLRP2-TLE6-OOEP complex

EntireName: Structure of human NLRP2-TLE6-OOEP complex
Components
  • Complex: Structure of human NLRP2-TLE6-OOEP complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 2
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog

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Supramolecule #1: Structure of human NLRP2-TLE6-OOEP complex

SupramoleculeName: Structure of human NLRP2-TLE6-OOEP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NACHT, LRR and PYD domains-containing protein 2

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.666141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSSAQMGFN LQALLEQLSQ DELSKFKYLI TTFSLAHELQ KIPHKEVDKA DGKQLVEILT THCDSYWVEM ASLQVFEKMH RMDLSERAK DEVREAALKS FNKRKPLSLG ITRKERPPLD VDEMLERFKT EAQAFTETKG NVICLGKEVF KGKKPDKDNR C RYILKTKF ...String:
MVSSAQMGFN LQALLEQLSQ DELSKFKYLI TTFSLAHELQ KIPHKEVDKA DGKQLVEILT THCDSYWVEM ASLQVFEKMH RMDLSERAK DEVREAALKS FNKRKPLSLG ITRKERPPLD VDEMLERFKT EAQAFTETKG NVICLGKEVF KGKKPDKDNR C RYILKTKF REMWKSWPGD SKEVQVMAER YKMLIPFSNP RVLPGPFSYT VVLYGPAGLG KTTLAQKLML DWAEDNLIHK FK YAFYLSC RELSRLGPCS FAELVFRDWP ELQDDIPHIL AQARKILFVI DGFDELGAAP GALIEDICGD WEKKKPVPVL LGS LLNRVM LPKAALLVTT RPRALRDLRI LAEEPIYIRV EGFLEEDRRA YFLRHFGDED QAMRAFELMR SNAALFQLGS APAV CWIVC TTLKLQMEKG EDPVPTCLTR TGLFLRFLCS RFPQGAQLRG ALRTLSLLAA QGLWAQTSVL HREDLERLGV QESDL RLFL DGDILRQDRV SKGCYSFIHL SFQQFLTALF YTLEKEEEED RDGHTWDIGD VQKLLSGVER LRNPDLIQAG YYSFGL ANE KRAKELEATF GCRMSPDIKQ ELLRCDISCK GGHSTVTDLQ ELLGCLYESQ EEELVKEVMA QFKEISLHLN AVDVVPS SF CVKHCRNLQK MSLQVIKENL PENVTASESD AEVERSQDDQ HMLPFWTDLC SIFGSNKDLM GLAINDSFLS ASLVRILC E QIASDTCHLQ RVVFKNISPA DAHRNLCLAL RGHKTVTYLT LQGNDQDDMF PALCEVLRHP ECNLRYLGLV SCSATTQQW ADLSLALEVN QSLTCVNLSD NELLDEGAKL LYTTLRHPKC FLQRLSLENC HLTEANCKDL AAVLVVSREL THLCLAKNPI GNTGVKFLC EGLRYPECKL QTLVLWNCDI TSDGCCDLTK LLQEKSSLLC LDLGLNHIGV KGMKFLCEAL RKPLCNLRCL W LWGCSIPP FSCEDLCSAL SCNQSLVTLD LGQNPLGSSG VKMLFETLTC SSGTLRTLRL KIDDFNDELN KLLEEIEEKN PQ LIIDTEK HHPWAERPSS HDFMI

UniProtKB: NACHT, LRR and PYD domains-containing protein 2

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Macromolecule #2: Transducin-like enhancer protein 6

MacromoleculeName: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.541148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTSRDQPRPK GPPKSTSPCP GISNSESSPT LNYQGILNRL KQFPRFSPHF AAELESIYYS LHKIQQDVAE HHKQIGNVLQ IVESCSQLQ GFQSEEVSPA EPASPGTPQQ VKDKTLQESS FEDIMATRSS DWLRRPLGED NQPETQLFWD KEPWFWHDTL T EQLWRIFA ...String:
MTSRDQPRPK GPPKSTSPCP GISNSESSPT LNYQGILNRL KQFPRFSPHF AAELESIYYS LHKIQQDVAE HHKQIGNVLQ IVESCSQLQ GFQSEEVSPA EPASPGTPQQ VKDKTLQESS FEDIMATRSS DWLRRPLGED NQPETQLFWD KEPWFWHDTL T EQLWRIFA GVHDEKAKPR DRQQAPGLGQ ESKAPGSCDP GTDPCPEDAS TPRPPEASSS PPEGSQDRNT SWGVVQEPPG RA SRFLQSI SWDPEDFEDA WKRPDALPGQ SKRLAVPCKL EKMRILAHGE LVLATAISSF TRHVFTCGRR GIKVWSLTGQ VAE DRFPES HLPIQTPGAF LRTCLLSSNS RSLLTGGYNL ASVSVWDLAA PSLHVKEQLP CAGLNCQALD ANLDANLAFA SFTS GVVRI WDLRDQSVVR DLKGYPDGVK SIVVKGYNIW TGGPDACLRC WDQRTIMKPL EYQFKSQIMS LSHSPQEDWV LLGMA NGQQ WLQSTSGSQR HMVGQKDSVI LSVKFSPFGQ WWASVGMDDF LGVYSMPAGT KVFEVPEMSP VTCCDVSSNN RLVVTG SGE HASVYQITY

UniProtKB: Transducin-like enhancer protein 6

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Macromolecule #3: Oocyte-expressed protein homolog

MacromoleculeName: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.194756 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVDDAGAAES QRGKQTPAHS LEQLRRLPLP PPQIRIRPWW FPVQELRDPL VFYLEAWLAD ELFGPDRAII PEMEWTSQAL LTVDIVDSG NLVEITVFGR PRVQNRVKSM LLCLAWFHRE HRARAEKMKH LEKNLKAHAS DPHSPQDPVA

UniProtKB: Oocyte-expressed protein homolog

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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

Concentration2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.4 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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1347512
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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