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Yorodumi- PDB-9bq2: Structure of the flotillin complex in a native membrane environment -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bq2 | |||||||||
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Title | Structure of the flotillin complex in a native membrane environment | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Flotillin complex / SPFH / membrane interaction / endocytosis | |||||||||
Function / homology | Function and homology information plasma membrane raft assembly / regulation of neurotransmitter uptake / positive regulation of cell junction assembly / positive regulation of synaptic transmission, dopaminergic / plasma membrane raft organization / regulation of myoblast differentiation / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / protein kinase C signaling / dsRNA transport ...plasma membrane raft assembly / regulation of neurotransmitter uptake / positive regulation of cell junction assembly / positive regulation of synaptic transmission, dopaminergic / plasma membrane raft organization / regulation of myoblast differentiation / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / protein kinase C signaling / dsRNA transport / regulation of receptor internalization / uropod / dopaminergic synapse / positive regulation of skeletal muscle tissue development / Synaptic adhesion-like molecules / flotillin complex / cell-cell contact zone / regulation of Rho protein signal transduction / positive regulation of heterotypic cell-cell adhesion / microtubule organizing center / RIPK1-mediated regulated necrosis / RHOB GTPase cycle / positive regulation of myoblast fusion / cellular response to exogenous dsRNA / RHOC GTPase cycle / presynaptic active zone / positive regulation of endocytosis / centriolar satellite / RHOA GTPase cycle / extracellular matrix disassembly / GABA-ergic synapse / positive regulation of interferon-beta production / response to endoplasmic reticulum stress / axonogenesis / positive regulation of cytokine production / caveola / protein localization to plasma membrane / adherens junction / ionotropic glutamate receptor binding / Regulation of necroptotic cell death / sarcolemma / cell-cell junction / melanosome / positive regulation of protein binding / lamellipodium / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / protease binding / early endosome / protein stabilization / cell adhesion / endosome / positive regulation of protein phosphorylation / membrane raft / lysosomal membrane / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / glutamatergic synapse / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Fu, Z. / MacKinnon, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structure of the flotillin complex in a native membrane environment. Authors: Ziao Fu / Roderick MacKinnon / Abstract: In this study, we used cryoelectron microscopy to determine the structures of the Flotillin protein complex, part of the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) superfamily, from cell- ...In this study, we used cryoelectron microscopy to determine the structures of the Flotillin protein complex, part of the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) superfamily, from cell-derived vesicles without detergents. It forms a right-handed helical barrel consisting of 22 pairs of Flotillin1 and Flotillin2 subunits, with a diameter of 32 nm at its wider end and 19 nm at its narrower end. Oligomerization is stabilized by the C terminus, which forms two helical layers linked by a β-strand, and coiled-coil domains that enable strong charge-charge intersubunit interactions. Flotillin interacts with membranes at both ends; through its SPFH1 domains at the wide end and the C terminus at the narrow end, facilitated by hydrophobic interactions and lipidation. The inward tilting of the SPFH domain, likely triggered by phosphorylation, suggests its role in membrane curvature induction, which could be connected to its proposed role in clathrin-independent endocytosis. The structure suggests a shared architecture across the family of SPFH proteins and will promote further research into Flotillin's roles in cell biology. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bq2.cif.gz | 261.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bq2.ent.gz | 213.1 KB | Display | PDB format |
PDBx/mmJSON format | 9bq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bq2_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9bq2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9bq2_validation.xml.gz | 35 KB | Display | |
Data in CIF | 9bq2_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/9bq2 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/9bq2 | HTTPS FTP |
-Related structure data
Related structure data | 44792MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: C22 (22 fold cyclic)) |
-Components
#1: Protein | Mass: 44572.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: J3QLD9 |
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#2: Protein | Mass: 46880.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: O75955 |
-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: Flotillin complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C22 (22 fold cyclic) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1436 / Symmetry type: POINT |