[English] 日本語
Yorodumi
- EMDB-38128: Structure of human SCMC ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38128
TitleStructure of human SCMC ternary complex
Map data
Sample
  • Complex: human SCMC ternary complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
Keywordsoocyte / subcortical / complex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / establishment of organelle localization / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / cortical granule / positive regulation of embryonic development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins ...embryonic process involved in female pregnancy / subcortical maternal complex / establishment of organelle localization / cortical granule exocytosis / endoplasmic reticulum localization / establishment or maintenance of apical/basal cell polarity / cortical granule / positive regulation of embryonic development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / positive regulation of meiotic nuclear division / regulation of establishment of protein localization / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / mitochondrion localization / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / establishment of spindle localization / embryonic pattern specification / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / positive regulation of double-strand break repair / detection of maltose stimulus / maltose transport complex / exocytosis / replication fork processing / carbohydrate transport / ubiquitin-like protein ligase binding / regulation of cell division / protein sumoylation / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of double-strand break repair via homologous recombination / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / tubulin binding / ATP-binding cassette (ABC) transporter complex / condensed nuclear chromosome / actin filament organization / cell chemotaxis / negative regulation of canonical Wnt signaling pathway / protein tag activity / transcription corepressor activity / regulation of protein localization / outer membrane-bounded periplasmic space / cell cortex / regulation of inflammatory response / transcription regulator complex / periplasmic space / intracellular membrane-bounded organelle / DNA damage response / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / mitochondrion / RNA binding / ATP binding / identical protein binding / nucleus / membrane / 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 / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 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 / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like 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 / Maltose/maltodextrin-binding periplasmic protein / NACHT, LRR and PYD domains-containing protein 5 / Ubiquitin-like protein SMT3 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChi P / Ou G / Liu S / Lu Y / Li JH / Li JL / Wang X / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171211 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cryo-EM structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants.
Authors: Pengliang Chi / Guojin Ou / Sibei Liu / Qianhong Ma / Yuechao Lu / Jinhong Li / Jialu Li / Qianqian Qi / Zhuo Han / Zihan Zhang / Qingting Liu / Li Guo / Jing Chen / Xiang Wang / Wei Huang / ...Authors: Pengliang Chi / Guojin Ou / Sibei Liu / Qianhong Ma / Yuechao Lu / Jinhong Li / Jialu Li / Qianqian Qi / Zhuo Han / Zihan Zhang / Qingting Liu / Li Guo / Jing Chen / Xiang Wang / Wei Huang / Lei Li / Dong Deng /
Abstract: The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, ...The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants.
History
DepositionNov 26, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38128.png

Downloads & links

-
Map

FileDownload / File: emd_38128.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: 0.1
Minimum - Maximum-1.2158194 - 1.7158313
Average (Standard dev.)-0.00014587509 (±0.034783673)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_38128_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38128_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38128_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human SCMC ternary complex

EntireName: human SCMC ternary complex
Components
  • Complex: human SCMC ternary complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6

-
Supramolecule #1: human SCMC ternary complex

SupramoleculeName: human SCMC ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 171.393734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKGS MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE L KAKGKSAL ...String:
MDYKDDDDKG DYKDDDDKGS MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE L KAKGKSAL MFNLQEPYFT WPLIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NK GETAMTI NGPWAWSNID TSKVNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPL GAVALK SYEEELAKDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TLTFSSYGLQ WCLY ELDKE EFQTFKELLK KKSSESTTCS IPQFEIENAN VECLALLLHE YYGASLAWAT SISIFENMNL RTLSEKARDD MKRHS PEDP EATMTDQGPS KEKVPGISQA VQQDSATAAE TKEQEISQAM EQEGATAAET EEQEISQAME QEGATAAETE EQGHGG DTW DYKSHVMTKF AEEEDVRRSF ENTAADWPEM QTLAGAFDSD RWGFRPRTVV LHGKSGIGKS ALARRIVLCW AQGGLYQ GM FSYVFFLPVR EMQRKKESSV TEFISREWPD SQAPVTEIMS RPERLLFIID GFDDLGSVLN NDTKLCKDWA EKQPPFTL I RSLLRKVLLP ESFLIVTVRD VGTEKLKSEV VSPRYLLVRG ISGEQRIHLL LERGIGEHQK TQGLRAIMNN RELLDQCQV PAVGSLICVA LQLQDVVGES VAPFNQTLTG LHAAFVFHQL TPRGVVRRCL NLEERVVLKR FCRMAVEGVW NRKSVFDGDD LMVQGLGES ELRALFHMNI LLPDSHCEEY YTFFHLSLQD FCAALYYVLE GLEIEPALCP LYVEKTKRSM ELKQAGFHIH S LWMKRFLF GLVSEDVRRP LEVLLGCPVP LGVKQKLLHW VSLLGQQPNA TTPGDTLDAF HCLFETQDKE FVRLALNSFQ EV WLPINQN LDLIASSFCL QHCPYLRKIR VDVKGIFPRD ESAEACPVVP LWMRDKTLIE EQWEDFCSML GTHPHLRQLD LGS SILTER AMKTLCAKLR HPTCKIQTLM FRNAQITPGV QHLWRIVMAN RNLRSLNLGG THLKEEDVRM ACEALKHPKC LLES LRLDC CGLTHACYLK ISQILTTSPS LKSLSLAGNK VTDQGVMPLS DALRVSQCAL QKLILEDCGI TATGCQSLAS ALVSN RSLT HLCLSNNSLG NEGVNLLCRS MRLPHCSLQR LMLNQCHLDT AGCGFLALAL MGNSWLTHLS LSMNPVEDNG VKLLCE VMR EPSCHLQDLE LVKCHLTAAC CESLSCVISR SRHLKSLDLT DNALGDGGVA ALCEGLKQKN SVLARLGLKA CGLTSDC CE ALSLALSCNR HLTSLNLVQN NFSPKGMMKL CSAFACPTSN LQIIGLWKWQ YPVQIRKLLE EVQLLKPRVV IDGSWHSF D EDDRYWWKN

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, NACHT, LRR and PYD domains-containing protein 5

-
Macromolecule #2: Oocyte-expressed protein homolog

MacromoleculeName: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.479176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVDDAGAAES QRGKQTPAHS LEQLRRLPLP PPQIRIRPWW FPVQELRDPL VFYLEAWLAD ELFGPDRAII PEMEWTSQAL LTVDIVDSG NLVEITVFGR PRVQNRVKSM LLCLAWFHRE HRARAEKMKH LEKNLKAHAS DPHSPQDPVA LEWSHPQFEK

UniProtKB: Oocyte-expressed protein homolog

-
Macromolecule #3: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6

MacromoleculeName: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.899367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG TMSDSEVNQE AKPEVKPEVK PETHINLKVS DGSSEIFFKI KKTTPLRRLM EAFAKRQGKE MDSLRFLYDG IRIQADQTP EDLDMEDNDI IEAHREQIGG LFWDKEPWFW HDTLTEQLWR IFAGVHDEKA KPRDRQQAPG LGQESKAPGS C DPGTDPCP ...String:
MWSHPQFEKG TMSDSEVNQE AKPEVKPEVK PETHINLKVS DGSSEIFFKI KKTTPLRRLM EAFAKRQGKE MDSLRFLYDG IRIQADQTP EDLDMEDNDI IEAHREQIGG LFWDKEPWFW HDTLTEQLWR IFAGVHDEKA KPRDRQQAPG LGQESKAPGS C DPGTDPCP EDASTPRPPE ASSSPPEGSQ DRNTSWGVVQ EPPGRASRFL QSISWDPEDF EDAWKRPDAL PGQSKRLAVP CK LEKMRIL AHGELVLATA ISSFTRHVFT CGRRGIKVWS LTGQVAEDRF PESHLPIQTP GAFLRTCLLS SNSRSLLTGG YNL ASVSVW DLAAPSLHVK EQLPCAGLNC QALDANLDAN LAFASFTSGV VRIWDLRDQS VVRDLKGYPD GVKSIVVKGY NIWT GGPDA CLRCWDQRTI MKPLEYQFKS QIMSLSHSPQ EDWVLLGMAN GQQWLQSTSG SQRHMVGQKD SVILSVKFSP FGQWW ASVG MDDFLGVYSM PAGTKVFEVP EMSPVTCCDV SSNNRLVVTG SGEHASVYQI TY

UniProtKB: Ubiquitin-like protein SMT3, Transducin-like enhancer protein 6

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.336 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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280159
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more