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- EMDB-50984: Endophilin B1 dimer bound to nanodisc center -

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Basic information

Entry
Database: EMDB / ID: EMD-50984
TitleEndophilin B1 dimer bound to nanodisc center
Map dataFocused map of an Endophilin B1 dimer bound to the center of a nanodisc
Sample
  • Complex: Endophilin B1 dimers bound to a nanodisc
    • Protein or peptide: Endophilin-B1
KeywordsBAR / N-BAR / endophilin / membrane / curvature / cardiolipin / MSP2N2 / nanodisc / peripheral membrane protein / APOPTOSIS
Function / homology
Function and homology information


lysophosphatidic acid acyltransferase activity / 'de novo' post-translational protein folding / positive regulation of membrane tubulation / phosphatidic acid biosynthetic process / autophagic cell death / protein localization to vacuolar membrane / positive regulation of autophagosome assembly / phosphatidylinositol 3-kinase activator activity / receptor catabolic process / membrane fission ...lysophosphatidic acid acyltransferase activity / 'de novo' post-translational protein folding / positive regulation of membrane tubulation / phosphatidic acid biosynthetic process / autophagic cell death / protein localization to vacuolar membrane / positive regulation of autophagosome assembly / phosphatidylinositol 3-kinase activator activity / 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 / fatty acid binding / regulation of cytokinesis / positive regulation of protein-containing complex assembly / regulation of protein stability / autophagy / cytoplasmic vesicle / midbody / mitochondrial outer membrane / nuclear body / cadherin binding / Golgi membrane / apoptotic process / protein homodimerization activity / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsThorlacius A / Sundborger-Lunna A
Funding support Sweden, 1 items
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, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50984.png

Downloads & links

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Map

FileDownload / File: emd_50984.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of an Endophilin B1 dimer bound to the center of a nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 339.968 Å		1.33 Å/pix.
x 256 pix.
= 339.968 Å		1.33 Å/pix.
x 256 pix.
= 339.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.4356274 - 0.9382321
Average (Standard dev.)0.00010833973 (±0.017875832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50984_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50984_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50984_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Endophilin B1 dimers bound to a nanodisc

EntireName: Endophilin B1 dimers bound to a nanodisc
Components
  • Complex: Endophilin B1 dimers bound to a nanodisc
    • Protein or peptide: Endophilin-B1

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Supramolecule #1: Endophilin B1 dimers bound to a nanodisc

SupramoleculeName: Endophilin B1 dimers bound to a nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Endophilin-B1

MacromoleculeName: Endophilin-B1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.843246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNIMDFNVKK LAADAGTFLS RAVQFTEEKL GQAEKTELDA HLENLLSKAE CTKIWTEKIM KQTEVLLQPN PNARIEEFVY EKLDRKAPS RINNPELLGQ YMIDAGTEFG PGTAYGNALI KCGETQKRIG TADRELIQTS ALNFLTPLRN FIEGDYKTIA K ERKLLQNK ...String:
MNIMDFNVKK LAADAGTFLS RAVQFTEEKL GQAEKTELDA HLENLLSKAE CTKIWTEKIM KQTEVLLQPN PNARIEEFVY EKLDRKAPS RINNPELLGQ YMIDAGTEFG PGTAYGNALI KCGETQKRIG TADRELIQTS ALNFLTPLRN FIEGDYKTIA K ERKLLQNK RLDLDAAKTR LKKAKAAETR NSSEQELRIT QSEFDRQAEI TRLLLEGISS THAHHLRCLN DFVEAQMTYY AQ CYQYMLD LQKQLGSFPS NYLSNNNQTS VTPVPSVLPN AIGSSAMAST SGLVITSPSN LSDLKECSGS RKARVLYDYD AAN STELSL LADEVITVFS VVGMDSDWLM GERGNQKGKV PITYLELLN

UniProtKB: Endophilin-B1

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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

Concentration1.8 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA, pH 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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 / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5026978
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 273120
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

l_v4


Chain - Chain ID: A / Chain - Residue range: 11-252 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsAlphafold model was processed in PHENIX, docked into the density map using UCSF Chimera, refined using all-chain refinement in coot followed by real-space refinement with Servalcat.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g2u:
Endophilin B1 dimer bound to nanodisc center

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