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- PDB-9bq2: Structure of the flotillin complex in a native membrane environment -

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Basic information

Entry
Database: PDB / ID: 9bq2
TitleStructure of the flotillin complex in a native membrane environment
Components
  • Flotillin-1
  • Flotillin-2
KeywordsMEMBRANE 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 / dsRNA transport / positive regulation of synaptic transmission, dopaminergic / plasma membrane raft organization / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / regulation of receptor internalization / uropod ...plasma membrane raft assembly / regulation of neurotransmitter uptake / positive regulation of cell junction assembly / dsRNA transport / positive regulation of synaptic transmission, dopaminergic / plasma membrane raft organization / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / regulation of receptor internalization / uropod / positive regulation of skeletal muscle tissue development / flotillin complex / cell-cell contact zone / dopaminergic synapse / Synaptic adhesion-like molecules / regulation of Rho protein signal transduction / positive regulation of heterotypic cell-cell adhesion / RIPK1-mediated regulated necrosis / positive regulation of myoblast fusion / RHOB GTPase cycle / cellular response to exogenous dsRNA / RHOC GTPase cycle / microtubule organizing center / positive regulation of endocytosis / presynaptic active zone / extracellular matrix disassembly / RHOA GTPase cycle / ionotropic glutamate receptor binding / axonogenesis / positive regulation of interferon-beta production / response to endoplasmic reticulum stress / protein localization to plasma membrane / positive regulation of cytokine production / GABA-ergic synapse / adherens junction / sarcolemma / caveola / Regulation of necroptotic cell death / centriolar satellite / positive regulation of protein binding / melanosome / cell-cell junction / lamellipodium / positive regulation of protein phosphorylation / protease binding / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome / protein stabilization / intracellular signal transduction / membrane raft / external side of plasma membrane / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Flotillin family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Flotillin / Flotillin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFu, Z. / MacKinnon, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM43949 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionMay 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flotillin-2
B: Flotillin-1


Theoretical massNumber of molelcules
Total (without water)91,4532
Polymers91,4532
Non-polymers00
Water00
1
A: Flotillin-2
B: Flotillin-1
x 22


Theoretical massNumber of molelcules
Total (without water)2,011,96144
Polymers2,011,96144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation21
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C22 (22 fold cyclic))

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Components

#1: Protein Flotillin-2 / Flotillin


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
#2: Protein Flotillin-1


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

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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: Flotillin complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C22 (22 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1436 / Symmetry type: POINT

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