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- EMDB-44792: Structure of the flotillin complex in a native membrane environment -

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Basic information

Entry
Database: EMDB / ID: EMD-44792
TitleStructure of the flotillin complex in a native membrane environment
Map data
Sample
  • Complex: Flotillin complex
    • Protein or peptide: Flotillin-2
    • Protein or peptide: Flotillin-1
KeywordsFlotillin complex / SPFH / membrane interaction / endocytosis / MEMBRANE PROTEIN
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 / 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 ...plasma membrane raft assembly / regulation of neurotransmitter uptake / positive regulation of cell junction assembly / 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 / protein kinase C signaling / dsRNA transport / regulation of receptor internalization / uropod / positive regulation of skeletal muscle tissue development / Synaptic adhesion-like molecules / dopaminergic synapse / flotillin complex / cell-cell contact zone / regulation of Rho protein signal transduction / positive regulation of heterotypic cell-cell adhesion / microtubule organizing center / cellular response to exogenous dsRNA / RIPK1-mediated regulated necrosis / positive regulation of myoblast fusion / RHOB GTPase cycle / RHOC GTPase cycle / presynaptic active zone / positive regulation of endocytosis / centriolar satellite / extracellular matrix disassembly / RHOA GTPase cycle / GABA-ergic synapse / ionotropic glutamate receptor binding / response to endoplasmic reticulum stress / positive regulation of interferon-beta production / axonogenesis / positive regulation of cytokine production / protein localization to plasma membrane / adherens junction / caveola / Regulation of necroptotic cell death / sarcolemma / cell-cell junction / melanosome / positive regulation of protein binding / lamellipodium / cytoplasmic vesicle / basolateral plasma membrane / protease binding / positive regulation of canonical NF-kappaB signal transduction / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFu Z / MacKinnon R
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44792.png

Downloads & links

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Map

FileDownload / File: emd_44792.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 400 pix.
= 478.4 Å		1.2 Å/pix.
x 400 pix.
= 478.4 Å		1.2 Å/pix.
x 400 pix.
= 478.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.196 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.014062149 - 1.8432298
Average (Standard dev.)0.0018387123 (±0.029463831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 478.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_44792_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_44792_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_44792_half_map_2.map
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Sample components

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Entire : Flotillin complex

EntireName: Flotillin complex
Components
  • Complex: Flotillin complex
    • Protein or peptide: Flotillin-2
    • Protein or peptide: Flotillin-1

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Supramolecule #1: Flotillin complex

SupramoleculeName: Flotillin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Flotillin-2

MacromoleculeName: Flotillin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.572133 KDa
SequenceString: MGNCHTVGPN EALVVSGGCC GSDYKQYVFG GWAWAWWCIS DTQRLSLEVM TILCRCENIE TSEGVPLFVT GVAQVKIMTE KELLAVACE QFLGKNVQDI KNVVLQTLEG HLRSILGTLT VEQIYQDRDQ FAKLVREVAA PDVGRMGIEI LSFTIKDVYD K VDYLSSLG ...String:
MGNCHTVGPN EALVVSGGCC GSDYKQYVFG GWAWAWWCIS DTQRLSLEVM TILCRCENIE TSEGVPLFVT GVAQVKIMTE KELLAVACE QFLGKNVQDI KNVVLQTLEG HLRSILGTLT VEQIYQDRDQ FAKLVREVAA PDVGRMGIEI LSFTIKDVYD K VDYLSSLG KTQTAVVQRD ADIGVAEAER DAGIREAECK KEMLDVKFMA DTKIADSKRA FELQKSAFSE EVNIKTAEAQ LA YELQGAR EQQKIRQEEI EIEVVQRKKQ IAVEAQEILR TDKELIATVR RPAEAEAHRI QQIAEGEKVK QVLLAQAEAE KIR KIGEAE AAVIEAMGKA EAERMKLKAE AYQKYGDAAK MALVLEALPQ IAAKIAAPLT KVDEIVVLSG DNSKVTSEVN RLLA EL

UniProtKB: Flotillin

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Macromolecule #2: Flotillin-1

MacromoleculeName: Flotillin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.880641 KDa
SequenceString: MFFTCGPNEA MVVSGFCRSP PVMVAGGRVF VLPCIQQIQR ISLNTLTLNV KSEKVYTRHG VPISVTGIAQ VKIQGQNKEM LAAACQMFL GKTEAEIAHI ALETLEGHQR AIMAHMTVEE IYKDRQKFSE QVFKVASSDL VNMGISVVSY TLKDIHDDQD Y LHSLGKAR ...String:
MFFTCGPNEA MVVSGFCRSP PVMVAGGRVF VLPCIQQIQR ISLNTLTLNV KSEKVYTRHG VPISVTGIAQ VKIQGQNKEM LAAACQMFL GKTEAEIAHI ALETLEGHQR AIMAHMTVEE IYKDRQKFSE QVFKVASSDL VNMGISVVSY TLKDIHDDQD Y LHSLGKAR TAQVQKDARI GEAEAKRDAG IREAKAKQEK VSAQYLSEIE MAKAQRDYEL KKAAYDIEVN TRRAQADLAY QL QVAKTKQ QIEEQRVQVQ VVERAQQVAV QEQEIARREK ELEARVRKPA EAERYKLERL AEAEKSQLIM QAEAEAASVR MRG EAEAFA IGARARAEAE QMAKKAEAFQ LYQEAAQLDM LLEKLPQVAE EISGPLTSAN KITLVSSGSG TMGAAKVTGE VLDI LTRLP ESVERLTGVS ISQVNHK

UniProtKB: Flotillin-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C22 (22 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1436
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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