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- PDB-9l3g: Structure of the flotillin complex -

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Basic information

Entry
Database: PDB / ID: 9l3g
TitleStructure of the flotillin complex
Components
  • Flotillin-1
  • Flotillin-2
KeywordsMEMBRANE PROTEIN / SPFH protein family / scaffold protein / membrane compartmentalization / membrane microdomain
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLu, M. / Gao, N.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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-1
a: Flotillin-2
B: Flotillin-1
b: Flotillin-2
I: Flotillin-1
i: Flotillin-2
N: Flotillin-1
n: Flotillin-2
C: Flotillin-1
c: Flotillin-2
D: Flotillin-1
d: Flotillin-2
J: Flotillin-1
j: Flotillin-2
O: Flotillin-1
o: Flotillin-2
E: Flotillin-1
e: Flotillin-2
H: Flotillin-1
h: Flotillin-2
Q: Flotillin-1
q: Flotillin-2
S: Flotillin-1
s: Flotillin-2
F: Flotillin-1
f: Flotillin-2
G: Flotillin-1
g: Flotillin-2
K: Flotillin-1
k: Flotillin-2
P: Flotillin-1
p: Flotillin-2
U: Flotillin-1
u: Flotillin-2
V: Flotillin-1
v: Flotillin-2
R: Flotillin-1
r: Flotillin-2
T: Flotillin-1
t: Flotillin-2
L: Flotillin-1
l: Flotillin-2
M: Flotillin-1
m: Flotillin-2


Theoretical massNumber of molelcules
Total (without water)2,168,90244
Polymers2,168,90244
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flotillin-1


Mass: 51463.359 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLOT1 / Production host: Homo sapiens (human) / References: UniProt: O75955
#2: Protein ...
Flotillin-2 / Epidermal surface antigen / ESA / Membrane component chromosome 17 surface marker 1


Mass: 47123.078 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLOT2, ESA1, M17S1 / Production host: Homo sapiens (human) / References: UniProt: Q14254
Has protein modificationN

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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: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10RELION4initial Euler assignment
11RELION4final Euler assignment
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25977 / Symmetry type: POINT

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