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- EMDB-38369: Structure of mouse SCMC-14-3-3gama complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38369
TitleStructure of mouse SCMC-14-3-3gama complex
Map data
Sample
  • Complex: mouse SCMC-14-3-3gama complex
    • Protein or peptide: 14-3-3 protein gamma
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog
KeywordsComplex / Oocyte subcortical / phosphorylation / 14-3-3 / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


subcortical maternal complex / regulation of localization / endoplasmic reticulum localization / establishment of organelle localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / ooplasm / spermatogonial cell division / myofibril assembly / cortical granule ...subcortical maternal complex / regulation of localization / endoplasmic reticulum localization / establishment of organelle localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / ooplasm / spermatogonial cell division / myofibril assembly / cortical granule / positive regulation of meiotic nuclear division / positive regulation of embryonic development / regulation of establishment of protein localization / establishment of spindle localization / regulation of RNA stability / mitochondrion localization / apical cortex / embryonic pattern specification / fertilization / positive regulation of double-strand break repair / positive regulation of neurogenesis / myofibril / replication fork processing / regulation of cell division / exocytosis / positive regulation of double-strand break repair via homologous recombination / stress fiber / positive regulation of neuron differentiation / embryo implantation / actin filament organization / animal organ morphogenesis / negative regulation of canonical Wnt signaling pathway / regulation of protein stability / platelet aggregation / transcription corepressor activity / protein localization / apical part of cell / regulation of protein localization / cell cortex / regulation of inflammatory response / protein-containing complex assembly / in utero embryonic development / transcription regulator complex / calcium ion binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / 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 ...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 / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / Leucine-rich repeat / EF-hand domain pair / Leucine-rich repeat domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / 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
EF-hand domain-containing protein / Oocyte-expressed protein homolog / NACHT, LRR and PYD domains-containing protein 5 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChi P / Han Z / Jiao H / Li J / Wang X / Hu H / 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 mouse SCMC-14-3-3gama complex
Authors: Chi P / Han Z / Jiao H / Li J / Wang X / Hu H / Deng D
History
DepositionDec 19, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38369.png

Downloads & links

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Map

FileDownload / File: emd_38369.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. 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: 0.022
Minimum - Maximum-0.08889586 - 0.15988073
Average (Standard dev.)-0.000009722351 (±0.00604275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_38369_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38369_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_38369_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 : mouse SCMC-14-3-3gama complex

EntireName: mouse SCMC-14-3-3gama complex
Components
  • Complex: mouse SCMC-14-3-3gama complex
    • Protein or peptide: 14-3-3 protein gamma
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Oocyte-expressed protein homolog

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Supramolecule #1: mouse SCMC-14-3-3gama complex

SupramoleculeName: mouse SCMC-14-3-3gama complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: 14-3-3 protein gamma

MacromoleculeName: 14-3-3 protein gamma / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.33659 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVDREQLVQK ARLAEQAERY DDMAAAMKNV TELNEPLSNE ERNLLSVAYK NVVGARRSSW RVISSIEQKT SADGNEKKIE MVRAYREKI EKELEAVCQD VLSLLDNYLI KNCSETQYES KVFYLKMKGD YYRYLAEVAT GEKRATVVES SEKAYSEAHE I SKEHMQPT ...String:
MVDREQLVQK ARLAEQAERY DDMAAAMKNV TELNEPLSNE ERNLLSVAYK NVVGARRSSW RVISSIEQKT SADGNEKKIE MVRAYREKI EKELEAVCQD VLSLLDNYLI KNCSETQYES KVFYLKMKGD YYRYLAEVAT GEKRATVVES SEKAYSEAHE I SKEHMQPT HPIRLGLALN YSVFYYEIQN APEQACHLAK TAFDDAIAEL DTLNEDSYKD STLIMQLLRD NLTLWTSDQQ DD DGGEGNN

UniProtKB: EF-hand domain-containing protein

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 119.819859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGPPEKDSKA ILKARGLEEE QKSESTMSPS ENVSRAILKD SGSEEVEQAS ERKMTSPEND SKSIQKDQGP EQEQTSETLQ SKEEDEVTE ADKDNGGDLQ DYKAHVIAKF DTSVDLHYDS PEMKLLSDAF KPYQKTFQPH TIILHGRPGV GKSALARSIV L GWAQGKLF ...String:
MGPPEKDSKA ILKARGLEEE QKSESTMSPS ENVSRAILKD SGSEEVEQAS ERKMTSPEND SKSIQKDQGP EQEQTSETLQ SKEEDEVTE ADKDNGGDLQ DYKAHVIAKF DTSVDLHYDS PEMKLLSDAF KPYQKTFQPH TIILHGRPGV GKSALARSIV L GWAQGKLF QKMSFVIFFS VREIKWTEKS SLAQLIAKEC PDSWDLVTKI MSQPERLLFV IDGLDDMDSV LQHDDMTLSR DW KDEQPIY ILMYSLLRKA LLPQSFLIIT TRNTGLEKLK SMVVSPLYIL VEGLSASRRS QLVLENISNE SDRIQVFHSL IEN HQLFDQ CQAPSVCSLV CEALQLQKKL GKRCTLPCQT LTGLYATLVF HQLTLKRPSQ SALSQEEQIT LVGLCMMAAE GVWT MRSVF YDDDLKNYSL KESEILALFH MNILLQVGHN SEQCYVFSHL SLQDFFAALY YVLEGLEEWN QHFCFIENQR SIMEV KRTD DTRLLGMKRF LFGLMNKDIL KTLEVLFEYP VIPTVEQKLQ HWVSLIAQQV NGTSPMDTLD AFYCLFESQD EEFVGG ALK RFQEVWLLIN QKMDLKVSSY CLKHCQNLKA IRVDIRDLLS VDNTLELCPV VTVQETQCKP LLMEWWGNFC SVLGSLR NL KELDLGDSIL SQRAMKILCL ELRNQSCRIQ KLTFKSAEVV SGLKHLWKLL FSNQNLKYLN LGNTPMKDDD MKLACEAL K HPKCSVETLR LDSCELTIIG YEMISTLLIS TTRLKCLSLA KNRVGVKSMI SLGNALSSSM CLLQKLILDN CGLTPASCH LLVSALFSNQ NLTHLCLSNN SLGTEGVQQL CQFLRNPECA LQRLILNHCN IVDDAYGFLA MRLANNTKLT HLSLTMNPVG DGAMKLLCE ALKEPTCYLQ ELELVDCQLT QNCCEDLACM ITTTKHLKSL DLGNNALGDK GVITLCEGLK QSSSSLRRLG L GACKLTSN CCEALSLAIS CNPHLNSLNL VKNDFSTSGM LKLCSAFQCP VSNLGIIGLW KQEYYARVRR QLEEVEFVKP HV VIDGDWY ASDEDDRNWW KN

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

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Macromolecule #3: Transducin-like enhancer protein 6

MacromoleculeName: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 62.304711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKS GDEVDAGSGH IFSLAENFFQ AIERFSRTPD LLERNKMSIG VGAEGDSWPC HVSHEAPMGS AQTTENSAKE EDKQVPESA ALQHPKFKST PGPQLPTRRR FL(SEP)ESDELQD PQPVWDAEPQ FCQGFLIQGL WELFMDSRQK NQQEHGG ED SSQESKDSGL ...String:
MWSHPQFEKS GDEVDAGSGH IFSLAENFFQ AIERFSRTPD LLERNKMSIG VGAEGDSWPC HVSHEAPMGS AQTTENSAKE EDKQVPESA ALQHPKFKST PGPQLPTRRR FL(SEP)ESDELQD PQPVWDAEPQ FCQGFLIQGL WELFMDSRQK NQQEHGG ED SSQESKDSGL CDFKPEPQPR HRN(SEP)LSDSAD PFLIKSPSAL LDYYQEDVSR PQPETQESSG RADKFLKPLS WGSE VLESS CNQPSTALWQ LERFTVPQAL QKVRVLKHQE LLLVVAVSSF TRHVFTCSQS GIKVWNLVNQ VAEDRDPESH LKCSV QDNK VYLRTCLLSS NSRTLFAGGY NLPGVIVWDL AAPSLYEKCQ LPCEGLSCQA LANTKENMAL AGFTDGTVRI WDLRTQ EIV RNLKGPTNSA RNLVVKDDNI WTGGLDACLR CWDLRMAKVS LEHLFQSQIM SLAHSPTEDW LLLGLANGQH CLFNSRK RD QVLTVDTKDN TILGLKFSPN GKWWASVGMG NFITVHSMPT GAKLFQVPEV GPVRCFDMTE NGRLIITGSR DCASVYHI K Y

UniProtKB: Transducin-like enhancer protein 6

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Macromolecule #4: Oocyte-expressed protein homolog

MacromoleculeName: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 19.765717 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASHTADADA KPDSDSQKLL NVLPVSLRLR TRPWWFPIQE VSNPLVLYME AWVAERVIGT DQAEISEIEW MCQALLTVDS VNSGNLAEI TIFGQPSAQT RMKNILLNMA AWHKENELQR AVKVKEVEEF LKIRASSILS KLSKKGLKLA GFPLPLEGRE T QMESLEWS HPQFEK

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

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.15 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41406
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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