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- EMDB-62785: Structure of the flotillin complex -

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ID or keywords:

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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 / protein localization to plasma membrane raft / regulation of neurotransmitter uptake / positive regulation of cell junction assembly / dsRNA transport / anterograde dendritic transport / plasma membrane raft organization / regulation of myoblast differentiation / positive regulation of synaptic transmission, dopaminergic / positive regulation of toll-like receptor 3 signaling pathway ...plasma membrane raft assembly / protein localization to plasma membrane raft / regulation of neurotransmitter uptake / positive regulation of cell junction assembly / dsRNA transport / anterograde dendritic transport / plasma membrane raft organization / regulation of myoblast differentiation / positive regulation of synaptic transmission, dopaminergic / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / acrosomal membrane / regulation of receptor internalization / uropod / positive regulation of skeletal muscle tissue development / negative regulation of amyloid precursor protein catabolic process / flotillin complex / cell-cell contact zone / Synaptic adhesion-like molecules / regulation of Rho protein signal transduction / dopaminergic synapse / positive regulation of establishment of T cell polarity / positive regulation of heterotypic cell-cell adhesion / presynaptic active zone / RND1 GTPase cycle / RND3 GTPase cycle / RIPK1-mediated regulated necrosis / positive regulation of myoblast fusion / RHOB GTPase cycle / cellular response to exogenous dsRNA / RHOC GTPase cycle / microtubule organizing center / extracellular matrix disassembly / positive regulation of endocytosis / RHOA GTPase cycle / endocytic vesicle / epidermis development / positive regulation of protein binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / axonogenesis / positive regulation of interferon-beta production / response to endoplasmic reticulum stress / positive regulation of cytokine production / protein localization to plasma membrane / adherens junction / sarcolemma / caveola / GABA-ergic synapse / Regulation of necroptotic cell death / centriolar satellite / positive regulation of protein phosphorylation / 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 / negative regulation of gene expression / lysosomal membrane / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / 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: To Be Published
Title: Molecular mechanisms of flotillin complexes in organizing membrane microdomains
Authors: Lu M / Gao N
History
DepositionDec 18, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing 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
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62785_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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