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- EMDB-62815: Structure of human SCMCcore complex contain NLRP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-62815
TitleStructure of human SCMCcore complex contain NLRP2
Map data
Sample
  • Complex: human SCMCcore complex contains NLRP2
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 2
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Transducin-like enhancer protein 6
Keywordscomplex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / Pyrin domain binding / establishment of organelle localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity ...embryonic process involved in female pregnancy / subcortical maternal complex / Pyrin domain binding / establishment of organelle localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / cortical granule / positive regulation of embryonic development / positive regulation of meiotic nuclear division / regulation of establishment of protein localization / mitochondrion localization / embryonic pattern specification / establishment of spindle localization / flagellated sperm motility / epigenetic programming in the zygotic pronuclei / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of double-strand break repair / exocytosis / replication fork processing / regulation of cell division / positive regulation of double-strand break repair via homologous recombination / sperm midpiece / tubulin binding / 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 / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / mitochondrion / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
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 / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / 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 / NACHT, LRR and PYD domains-containing protein 5 / 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: 3.4 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: Structural assembly of 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_62815.png

Downloads & links

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Map

FileDownload / File: emd_62815.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0018
Minimum - Maximum-0.008884645 - 0.024493232
Average (Standard dev.)-0.000021552716 (±0.00047955164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62815_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_62815_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 : human SCMCcore complex contains NLRP2

EntireName: human SCMCcore complex contains NLRP2
Components
  • Complex: human SCMCcore complex contains NLRP2
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 2
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Transducin-like enhancer protein 6

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Supramolecule #1: human SCMCcore complex contains NLRP2

SupramoleculeName: human SCMCcore complex contains NLRP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 229.09 kDa/nm

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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: NACHT, LRR and PYD domains-containing protein 5

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 134.499688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVAGGLELG AAALLSASPR ALVTLSTGPT CSILPKNPLF PQNLSSQPCI KMEGDKSLTF SSYGLQWCLY ELDKEEFQTF KELLKKKSS ESTTCSIPQF EIENANVECL ALLLHEYYGA SLAWATSISI FENMNLRTLS EKARDDMKRH SPEDPEATMT D QGPSKEKV ...String:
MKVAGGLELG AAALLSASPR ALVTLSTGPT CSILPKNPLF PQNLSSQPCI KMEGDKSLTF SSYGLQWCLY ELDKEEFQTF KELLKKKSS ESTTCSIPQF EIENANVECL ALLLHEYYGA SLAWATSISI FENMNLRTLS EKARDDMKRH SPEDPEATMT D QGPSKEKV PGISQAVQQD SATAAETKEQ EISQAMEQEG ATAAETEEQE ISQAMEQEGA TAAETEEQGH GGDTWDYKSH VM TKFAEEE DVRRSFENTA ADWPEMQTLA GAFDSDRWGF RPRTVVLHGK SGIGKSALAR RIVLCWAQGG LYQGMFSYVF FLP VREMQR KKESSVTEFI SREWPDSQAP VTEIMSRPER LLFIIDGFDD LGSVLNNDTK LCKDWAEKQP PFTLIRSLLR KVLL PESFL IVTVRDVGTE KLKSEVVSPR YLLVRGISGE QRIHLLLERG IGEHQKTQGL RAIMNNRELL DQCQVPAVGS LICVA LQLQ DVVGESVAPF NQTLTGLHAA FVFHQLTPRG VVRRCLNLEE RVVLKRFCRM AVEGVWNRKS VFDGDDLMVQ GLGESE LRA LFHMNILLPD SHCEEYYTFF HLSLQDFCAA LYYVLEGLEI EPALCPLYVE KTKRSMELKQ AGFHIHSLWM KRFLFGL VS EDVRRPLEVL LGCPVPLGVK QKLLHWVSLL GQQPNATTPG DTLDAFHCLF ETQDKEFVRL ALNSFQEVWL PINQNLDL I ASSFCLQHCP YLRKIRVDVK GIFPRDESAE ACPVVPLWMR DKTLIEEQWE DFCSMLGTHP HLRQLDLGSS ILTERAMKT LCAKLRHPTC KIQTLMFRNA QITPGVQHLW RIVMANRNLR SLNLGGTHLK EEDVRMACEA LKHPKCLLES LRLDCCGLTH ACYLKISQI LTTSPSLKSL SLAGNKVTDQ GVMPLSDALR VSQCALQKLI LEDCGITATG CQSLASALVS NRSLTHLCLS N NSLGNEGV NLLCRSMRLP HCSLQRLMLN QCHLDTAGCG FLALALMGNS WLTHLSLSMN PVEDNGVKLL CEVMREPSCH LQ DLELVKC HLTAACCESL SCVISRSRHL KSLDLTDNAL GDGGVAALCE GLKQKNSVLA RLGLKACGLT SDCCEALSLA LSC NRHLTS LNLVQNNFSP KGMMKLCSAF ACPTSNLQII GLWKWQYPVQ IRKLLEEVQL LKPRVVIDGS WHSFDEDDRY WWKN

UniProtKB: NACHT, LRR and PYD domains-containing protein 5

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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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Macromolecule #4: Transducin-like enhancer protein 6

MacromoleculeName: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 4 / 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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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
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTrisTris(hydroxymethyl)aminomethane
5.0 mMDTTDithiothreitol

Details: 25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in argon atmosphere.
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: 1.2 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3186536
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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