[English] 日本語
Yorodumi
- PDB-9l3g: Structure of the flotillin complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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)
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: 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, 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
Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 2.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more