- EMDB-12700: Structure of the C9orf72-SMCR8 complex -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-12700
Title
Structure of the C9orf72-SMCR8 complex
Map data
Map of C9orf72-SMCR8 complex
Sample
Complex: C9orf72-SMCR8 complex
Protein or peptide: Ubiquitin-like protein SMT3,Guanine nucleotide exchange C9orf72
Protein or peptide: Guanine nucleotide exchange protein SMCR8,Guanine nucleotide exchange protein SMCR8,Maltose/maltodextrin-binding periplasmic protein
Function / homology
Function and homology information
Atg1/ULK1 kinase complex / 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 / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / late endosome to lysosome transport / SUMOylation of transcription cofactors / regulation of TORC1 signaling ...Atg1/ULK1 kinase complex / 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 / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / late endosome to lysosome transport / SUMOylation of transcription cofactors / regulation of TORC1 signaling / SUMOylation of DNA damage response and repair proteins / regulation of autophagosome assembly / negative regulation of autophagosome assembly / SUMOylation of DNA replication proteins / regulation of actin filament organization / septin ring / guanyl-nucleotide exchange factor complex / SUMOylation of SUMOylation proteins / negative regulation of immune response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / axon extension / Flemming body / negative regulation of exocytosis / positive regulation of autophagosome maturation / SUMOylation of chromatin organization proteins / main axon / negative regulation of macroautophagy / detection of maltose stimulus / maltose transport complex / protein kinase inhibitor activity / ubiquitin-like protein ligase binding / carbohydrate transport / positive regulation of macroautophagy / protein sumoylation / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of TOR signaling / autophagosome / axonal growth cone / stress granule assembly / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / GTPase activator activity / guanyl-nucleotide exchange factor activity / cell chemotaxis / positive regulation of GTPase activity / negative regulation of protein phosphorylation / condensed nuclear chromosome / regulation of autophagy / cell projection / negative regulation of protein kinase activity / P-body / PML body / small GTPase binding / autophagy / cytoplasmic stress granule / endocytosis / protein tag activity / regulation of protein localization / presynapse / outer membrane-bounded periplasmic space / postsynapse / perikaryon / nuclear membrane / periplasmic space / lysosome / endosome / negative regulation of gene expression / intracellular membrane-bounded organelle / DNA damage response / dendrite / chromatin / protein kinase binding / extracellular space / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
Guanine nucleotide exchange factor C9orf72 / C9orf72-like protein family / Tripartite DENN C9ORF72-type domain profile. / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Guanine nucleotide exchange factor C9orf72 / C9orf72-like protein family / Tripartite DENN C9ORF72-type domain profile. / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Ubiquitin-like protein SMT3 / Guanine nucleotide exchange protein SMCR8 / Guanine nucleotide exchange factor C9orf72 Similarity search - Component
Biological species
Homo sapiens (human) / Escherichia coli K-12 (bacteria)
Journal: PLoS Biol / Year: 2021 Title: Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture. Authors: Julia Nörpel / Simone Cavadini / Andreas D Schenk / Alexandra Graff-Meyer / Daniel Hess / Jan Seebacher / Jeffrey A Chao / Varun Bhaskar / Abstract: A major cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) spectrum disorder is the hexanucleotide G4C2 repeat expansion in the first intron of the C9orf72 gene. ...A major cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) spectrum disorder is the hexanucleotide G4C2 repeat expansion in the first intron of the C9orf72 gene. Many underlying mechanisms lead to manifestation of disease that include toxic gain-of-function by repeat G4C2 RNAs, dipeptide repeat proteins, and a reduction of the C9orf72 gene product. The C9orf72 protein interacts with SMCR8 and WDR41 to form a trimeric complex and regulates multiple cellular pathways including autophagy. Here, we report the structure of the C9orf72-SMCR8 complex at 3.8 Å resolution using single-particle cryo-electron microscopy (cryo-EM). The structure reveals 2 distinct dimerization interfaces between C9orf72 and SMCR8 that involves an extensive network of interactions. Homology between C9orf72-SMCR8 and Folliculin-Folliculin Interacting Protein 2 (FLCN-FNIP2), a GTPase activating protein (GAP) complex, enabled identification of a key residue within the active site of SMCR8. Further structural analysis suggested that a coiled-coil region within the uDenn domain of SMCR8 could act as an interaction platform for other coiled-coil proteins, and its deletion reduced the interaction of the C9orf72-SMCR8 complex with FIP200 upon starvation. In summary, this study contributes toward our understanding of the biological function of the C9orf72-SMCR8 complex.
History
Deposition
Mar 31, 2021
-
Header (metadata) release
Jul 21, 2021
-
Map release
Jul 21, 2021
-
Update
Feb 2, 2022
-
Current status
Feb 2, 2022
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Protein or peptide: Ubiquitin-like protein SMT3,Guanine nucleotide exchange C9orf72
Protein or peptide: Guanine nucleotide exchange protein SMCR8,Guanine nucleotide exchange protein SMCR8,Maltose/maltodextrin-binding periplasmic protein
Macromolecule #2: Guanine nucleotide exchange protein SMCR8,Guanine nucleotide exch...
Macromolecule
Name: Guanine nucleotide exchange protein SMCR8,Guanine nucleotide exchange protein SMCR8,Maltose/maltodextrin-binding periplasmic protein type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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