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- PDB-8x7v: Structure of human SCMC ternary complex -

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Basic information

Entry
Database: PDB / ID: 8x7v
TitleStructure of human SCMC ternary complex
Components
  • Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
  • Oocyte-expressed protein homolog
  • Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6
KeywordsCYTOSOLIC PROTEIN / oocyte / subcortical / complex
Function / homology
Function and homology information


embryonic process involved in female pregnancy / subcortical maternal complex / regulation of localization / establishment of organelle localization / endoplasmic reticulum localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / SUMO is conjugated to E1 (UBA2:SAE1) / cortical granule / SUMOylation of nuclear envelope proteins ...embryonic process involved in female pregnancy / subcortical maternal complex / regulation of localization / establishment of organelle localization / endoplasmic reticulum localization / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / SUMO is conjugated to E1 (UBA2:SAE1) / cortical granule / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / positive regulation of meiotic nuclear division / SUMO is proteolytically processed / positive regulation of embryonic development / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / regulation of establishment of protein localization / establishment of spindle localization / septin ring / mitochondrion localization / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / 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 / replication fork processing / maltose transport complex / regulation of cell division / ubiquitin-like protein ligase binding / exocytosis / carbohydrate transport / protein sumoylation / positive regulation of double-strand break repair via homologous recombination / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / tubulin binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / actin filament organization / condensed nuclear chromosome / 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 / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / RNA binding / ATP binding / identical protein binding / membrane / 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 / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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 speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChi, P. / Ou, G. / Liu, S. / Lu, Y. / Li, J.H. / Li, J.L. / Wang, X. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171211 China
CitationJournal: To Be Published
Title: Structure of human SCMC ternary complex
Authors: Chi, P. / Ou, G. / Liu, S. / Lu, Y. / Li, J.H. / Li, J.L. / Wang, X. / Deng, D.
History
DepositionNov 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 5
B: Oocyte-expressed protein homolog
C: Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6


Theoretical massNumber of molelcules
Total (without water)249,7723
Polymers249,7723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 171393.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K-12 / Gene: malE, NLRP5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P59047
#2: Protein Oocyte-expressed protein homolog


Mass: 18479.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OOEP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A6NGQ2
#3: Protein Ubiquitin-like protein SMT3,Transducin-like enhancer protein 6


Mass: 59899.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: S288c / Gene: SMT3, TLE6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q12306, UniProt: Q9H808
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human SCMC ternary complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 51.336 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280159 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411455
ELECTRON MICROSCOPYf_angle_d0.64215515
ELECTRON MICROSCOPYf_dihedral_angle_d4.771517
ELECTRON MICROSCOPYf_chiral_restr0.0441747
ELECTRON MICROSCOPYf_plane_restr0.0041968

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