+Open data
-Basic information
Entry | Database: PDB / ID: 7mge | ||||||
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Title | Structure of C9orf72:SMCR8:WDR41 in complex with ARF1 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / complex / autophagy / ALS / GAP / small GTPase | ||||||
Function / homology | Function and homology information mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Atg1/ULK1 kinase complex / Glycosphingolipid transport / regulation of receptor internalization / late endosome to lysosome transport / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / regulation of TORC1 signaling / Synthesis of PIPs at the Golgi membrane ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Atg1/ULK1 kinase complex / Glycosphingolipid transport / regulation of receptor internalization / late endosome to lysosome transport / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / regulation of TORC1 signaling / Synthesis of PIPs at the Golgi membrane / negative regulation of autophagosome assembly / regulation of actin filament organization / guanyl-nucleotide exchange factor complex / regulation of autophagosome assembly / negative regulation of immune response / Nef Mediated CD4 Down-regulation / dendritic spine organization / axon extension / presynaptic cytosol / Flemming body / negative regulation of exocytosis / positive regulation of autophagosome maturation / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / negative regulation of macroautophagy / main axon / Golgi Associated Vesicle Biogenesis / protein kinase inhibitor activity / cell leading edge / Synthesis of PIPs at the plasma membrane / positive regulation of macroautophagy / autophagosome / intracellular copper ion homeostasis / positive regulation of TOR signaling / COPI-mediated anterograde transport / axonal growth cone / stress granule assembly / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / GTPase activator activity / small monomeric GTPase / positive regulation of GTPase activity / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / regulation of autophagy / cell projection / intracellular protein transport / P-body / cellular response to virus / small GTPase binding / autophagy / cytoplasmic stress granule / endocytosis / regulation of protein localization / presynapse / nuclear membrane / perikaryon / postsynapse / endosome / postsynaptic density / lysosome / neuron projection / protein domain specific binding / Golgi membrane / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / dendrite / chromatin / GTP binding / protein kinase binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å | ||||||
Authors | Su, M.-Y. / Hurley, J.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for the ARF GAP activity and specificity of the C9orf72 complex. Authors: Ming-Yuan Su / Simon A Fromm / Jonathan Remis / Daniel B Toso / James H Hurley / Abstract: Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 ...Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF bound to C9orf72:SMCR8:WDR41. The SMCR8 and C9orf72 domains form the binding pocket for ARF1. One face of the C9orf72 domain holds ARF1 in place, while the SMCR8 positions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required ~10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP. The structure also provides a model for the active forms of the longin domain GAPs of FLCN and NPRL2 that regulate the Rag GTPases of the mTORC1 pathway. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mge.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mge.ent.gz | 185.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mge_validation.pdf.gz | 799 KB | Display | wwPDB validaton report |
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Full document | 7mge_full_validation.pdf.gz | 815.8 KB | Display | |
Data in XML | 7mge_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 7mge_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/7mge ftp://data.pdbj.org/pub/pdb/validation_reports/mg/7mge | HTTPS FTP |
-Related structure data
Related structure data | 23827MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AE
#1: Protein | Mass: 51783.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR41, MSTP048 / Cell line (production host): HEK 293 GnTi / Production host: Homo sapiens (human) / References: UniProt: Q9HAD4 |
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#4: Protein | Mass: 18994.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Cell line (production host): HEK 293 GnTi / Production host: Homo sapiens (human) / References: UniProt: P84077 |
-Guanine nucleotide exchange ... , 2 types, 2 molecules BC
#2: Protein | Mass: 105149.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMCR8 / Cell line (production host): HEK 293 GnTi / Production host: Homo sapiens (human) / References: UniProt: Q8TEV9 |
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#3: Protein | Mass: 54391.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf72 / Cell line (production host): HEK 293 GnTi / Production host: Homo sapiens (human) / References: UniProt: Q96LT7 |
-Non-polymers , 3 types, 3 molecules
#5: Chemical | ChemComp-GDP / |
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#6: Chemical | ChemComp-BEF / |
#7: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of C9orf72:SMCR8:WDR41 with ARF1 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Units: MEGADALTONS / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: concentration range of 0.16-0.2 mg/ml |
Specimen support | Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: SerialEM / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 796219 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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