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- EMDB-62785: Structure of the flotillin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62785
TitleStructure of the flotillin complex
Map data
Sample
  • Complex: Flotillin complex
    • Protein or peptide: Flotillin-1
    • Protein or peptide: Flotillin-2
KeywordsSPFH protein family / scaffold protein / membrane compartmentalization / membrane microdomain / MEMBRANE PROTEIN
Function / homology
Function and homology information


plasma membrane raft assembly / positive regulation of cell junction assembly / protein localization to plasma membrane raft / regulation of neurotransmitter uptake / anterograde dendritic transport / plasma membrane raft organization / regulation of myoblast differentiation / positive regulation of synaptic transmission, dopaminergic / caveola assembly / positive regulation of cell-cell adhesion mediated by cadherin ...plasma membrane raft assembly / positive regulation of cell junction assembly / protein localization to plasma membrane raft / regulation of neurotransmitter uptake / anterograde dendritic transport / plasma membrane raft organization / regulation of myoblast differentiation / positive regulation of synaptic transmission, dopaminergic / caveola assembly / positive regulation of cell-cell adhesion mediated by cadherin / acrosomal membrane / uropod / regulation of receptor internalization / negative regulation of amyloid precursor protein catabolic process / flotillin complex / cell-cell contact zone / Synaptic adhesion-like molecules / cell-cell adhesion mediated by cadherin / adherens junction organization / dopaminergic synapse / regulation of Rho protein signal transduction / positive regulation of establishment of T cell polarity / RND1 GTPase cycle / presynaptic active zone / RND3 GTPase cycle / RIPK1-mediated regulated necrosis / RHOB GTPase cycle / RHOC GTPase cycle / microtubule organizing center / extracellular matrix disassembly / RHOA GTPase cycle / positive regulation of endocytosis / epidermis development / endocytic vesicle / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / axonogenesis / protein localization to plasma membrane / adherens junction / sarcolemma / caveola / Regulation of necroptotic cell death / GABA-ergic synapse / centriolar satellite / cell-cell junction / melanosome / lamellipodium / protease binding / cytoplasmic vesicle / basolateral plasma membrane / vesicle / early endosome / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / endosome / intracellular signal transduction / protein stabilization / membrane raft / intracellular membrane-bounded organelle / negative regulation of gene expression / external side of plasma membrane / lysosomal membrane / focal adhesion / perinuclear region of cytoplasm / 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-1 / Flotillin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLu M / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92354306 China
CitationJournal: Nat Commun / Year: 2026
Title: Molecular mechanisms of flotillin complexes in organizing membrane microdomains.
Authors: Ming-Ao Lu / Yunwen Qian / Liangwen Ma / Jinzhi Hong / Xiaopeng Li / Li Yu / Qiang Guo / Ning Gao /
Abstract: Flotillin-1 and flotillin-2 form hetero-oligomers to create flotillin membrane microdomains essential for endocytosis and protein sorting. However, the mechanisms of flotillin oligomerization and ...Flotillin-1 and flotillin-2 form hetero-oligomers to create flotillin membrane microdomains essential for endocytosis and protein sorting. However, the mechanisms of flotillin oligomerization and microdomain organization remain incompletely understood. Here, we present the cryo-EM structure of human flotillin complex, showing that flotillin-1 and -2 form a 44-mer, membrane attached, and dome-shaped structure that defines a 30-nm circular membrane domain. The cryo-ET data demonstrates that while attached to the cytoplasmic leaflet, flotillin complexes possess intrinsic structural plasticity in situ on the native membrane. Each flotillin complex may represent a fundamental unit of membrane microdomains, with their clustering enabling the formation of larger and more elaborate domains. We further reveal that phosphorylation at residues Y160 (flotillin-1) and Y163 (flotillin-2) may act as a molecular switch to modulate complex assembly, potentially regulating its function in endocytosis. These findings demonstrate the molecular mechanism of flotillin-mediated membrane segregation and microdomain formation, and suggest a previously unrecognized role of flotillin in sequestrating membrane proteins.
History
DepositionDec 18, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62785.png

Downloads & links

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Map

FileDownload / File: emd_62785.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 360 pix.
= 493.2 Å		1.37 Å/pix.
x 360 pix.
= 493.2 Å		1.37 Å/pix.
x 360 pix.
= 493.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.006743285 - 1.8352507
Average (Standard dev.)0.0030613686 (±0.040056713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 493.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62785_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62785_half_map_2.map
Projections & Slices
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Sample components

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Entire : Flotillin complex

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

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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-1

MacromoleculeName: Flotillin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.463359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 ISQVNHKPLR TAGITENLYF QGGSGDYKDH DGDYKDHDID YKDDDDK

UniProtKB: Flotillin-1

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Macromolecule #2: Flotillin-2

MacromoleculeName: Flotillin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.123078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNCHTVGPN EALVVSGGCC GSDYKQYVFG GWAWAWWCIS DTQRISLEIM TLQPRCEDVE TAEGVALTVT GVAQVKIMTE KELLAVACE QFLGKNVQDI KNVVLQTLEG HLRSILGTLT VEQIYQDRDQ FAKLVREVAA PDVGRMGIEI LSFTIKDVYD K VDYLSSLG ...String:
MGNCHTVGPN EALVVSGGCC GSDYKQYVFG GWAWAWWCIS DTQRISLEIM TLQPRCEDVE TAEGVALTVT 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 ELPAS VHALTGVDLS KIPLIKKATG VQV

UniProtKB: Flotillin-2

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25977
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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