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- PDB-9g2r: Endophilin B1 dimers bound to nanodiscs -

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Basic information

Entry
Database: PDB / ID: 9g2r
TitleEndophilin B1 dimers bound to nanodiscs
ComponentsEndophilin-B1
KeywordsAPOPTOSIS / BAR / N-BAR / endophilin / membrane / curvature / cardiolipin / MSP2N2 / nanodisc / peripheral membrane protein
Function / homology
Function and homology information


positive regulation of membrane tubulation / autophagic cell death / protein localization to vacuolar membrane / positive regulation of autophagosome assembly / receptor catabolic process / membrane fission / membrane organization / positive regulation of protein targeting to mitochondrion / autophagosome membrane / regulation of macroautophagy ...positive regulation of membrane tubulation / autophagic cell death / protein localization to vacuolar membrane / positive regulation of autophagosome assembly / receptor catabolic process / membrane fission / membrane organization / positive regulation of protein targeting to mitochondrion / autophagosome membrane / regulation of macroautophagy / cellular response to glucose starvation / positive regulation of autophagy / cellular response to amino acid starvation / regulation of cytokinesis / positive regulation of protein-containing complex assembly / regulation of protein stability / autophagy / midbody / cytoplasmic vesicle / mitochondrial outer membrane / nuclear body / cadherin binding / Golgi membrane / apoptotic process / lipid binding / protein homodimerization activity / protein-containing complex / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Endophilin-B1 / Endophilin-B1, BAR domain / BAR domain / BAR domain profile. / BAR / : / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains ...Endophilin-B1 / Endophilin-B1, BAR domain / BAR domain / BAR domain profile. / BAR / : / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsThorlacius, A. / Sundborger-Lunna, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2021-05423 Sweden
Citation
Journal: Commun Biol / Year: 2025
Title: Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers.
Authors: Arni Thorlacius / Maksim Rulev / Oscar Sundberg / Anna Sundborger-Lunna /
Abstract: Bin/Amphiphysin/Rvs167 (BAR) domain containing proteins are peripheral membrane proteins that regulate intracellular membrane curvature. BAR protein endophilin B1 plays a key role in multiple ...Bin/Amphiphysin/Rvs167 (BAR) domain containing proteins are peripheral membrane proteins that regulate intracellular membrane curvature. BAR protein endophilin B1 plays a key role in multiple cellular processes critical for oncogenesis, including autophagy and apoptosis. Amphipathic regions in endophilin B1 drive membrane association and tubulation through membrane scaffolding. Our understanding of exactly how BAR proteins like endophilin B1 promote highly diverse intracellular membrane remodeling events in the cell is severely limited due to lack of high-resolution structural information. Here we present the highest resolution cryo-EM structure of a BAR protein to date and the first structures of a BAR protein bound to a lipid bicelle. Using neural networks, we can effectively sort particle species of different stoichiometries, revealing the tremendous flexibility of post-membrane binding, pre-polymer BAR dimer organization and membrane deformation. We also show that endophilin B1 efficiently permeabilizes negatively charged liposomes that contain mitochondria-specific lipid cardiolipin and propose a new model for Bax-mediated cell death.
#1: Journal: Biorxiv / Year: 2024
Title: Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers
Authors: Thorlacius, A. / Rulev, M. / Sundberg, O. / Sundborger-Lunna, A.
History
DepositionJul 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_related
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.title / _citation.year / _em_admin.last_update
Revision 1.2Feb 19, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endophilin-B1
B: Endophilin-B1
C: Endophilin-B1
D: Endophilin-B1
E: Endophilin-B1
F: Endophilin-B1
G: Endophilin-B1
H: Endophilin-B1
I: Endophilin-B1
J: Endophilin-B1
K: Endophilin-B1
L: Endophilin-B1


Theoretical massNumber of molelcules
Total (without water)490,11912
Polymers490,11912
Non-polymers00
Water00
1


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

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Components

#1: Protein
Endophilin-B1 / Bax-interacting factor 1 / Bif-1 / SH3 domain-containing GRB2-like protein B1


Mass: 40843.246 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3GLB1, KIAA0491, CGI-61 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9Y371
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: Endophilin B1 dimers bound to a nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA, pH 7.4
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5026978
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273120 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Experimental models determined from locally refined maps were rigid body fitted into the consensus map.
Atomic model buildingAccession code: AF-Q9Y371-F1-model_v4 / Chain residue range: 11-252 / Source name: AlphaFold / Type: in silico model

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