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- EMDB-20835: Endophilin B1 helical scaffold -

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Basic information

Entry
Database: EMDB / ID: EMD-20835
TitleEndophilin B1 helical scaffold
Map dataEndophilin_N-BAR helical scaffolds assembled on tubulated liposomes
Sample
  • Complex: Endophilin B1 helical assembly
    • Protein or peptide: Endophilin-B1
KeywordsMembrane binding / amphipathic helix / BAR protein / SH3 domain / membrane trafficking / cell death / CYTOSOLIC 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 / positive regulation of autophagy / cellular response to glucose starvation / 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 / cadherin binding / Golgi membrane / lipid binding / apoptotic process / 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)
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsBhatt VS / Sundborger-Lunna AC
CitationJournal: Structure / Year: 2021
Title: Amphipathic Motifs Regulate N-BAR Protein Endophilin B1 Auto-inhibition and Drive Membrane Remodeling.
Authors: Veer S Bhatt / Robert Ashley / Anna Sundborger-Lunna /
Abstract: Membrane remodeling is a common theme in a variety of cellular processes. Here, we investigated membrane remodeling N-BAR protein endophilin B1, a critical player in diverse intracellular trafficking ...Membrane remodeling is a common theme in a variety of cellular processes. Here, we investigated membrane remodeling N-BAR protein endophilin B1, a critical player in diverse intracellular trafficking events, including mitochondrial and Golgi fission, and apoptosis. We find that endophilin B1 assembles into helical scaffolds on membranes, and that both membrane binding and assembly are driven by interactions between N-terminal helix H0 and the lipid bilayer. Furthermore, we find that endophilin B1 membrane remodeling is auto-inhibited and identify direct SH3 domain-H0 interactions as the underlying mechanism. Our results indicate that lipid composition plays a role in dictating endophilin B1 activity. Taken together, this study provides insight into a poorly understood N-BAR protein family member and highlights molecular mechanisms that may be general for the regulation of membrane remodeling. Our work suggests that interplay between membrane lipids and membrane interacting proteins facilitates spatial and temporal coordination of membrane remodeling.
History
DepositionOct 16, 2019-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6up6
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6up6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20835.png

Downloads & links

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Map

FileDownload / File: emd_20835.map.gz / Format: CCP4 / Size: 37.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEndophilin_N-BAR helical scaffolds assembled on tubulated liposomes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.29 Å/pix.
x 214 pix.
= 490.06 Å		2.29 Å/pix.
x 214 pix.
= 490.06 Å		2.29 Å/pix.
x 214 pix.
= 490.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.017276157 - 0.036517918
Average (Standard dev.)0.002104759 (±0.0067668124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214214
Spacing214214214
CellA=B=C: 490.06 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.292.292.29
M x/y/z214214214
origin x/y/z0.0000.0000.000
length x/y/z490.060490.060490.060
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS214214214
D min/max/mean-0.0170.0370.002

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Supplemental data

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Sample components

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Entire : Endophilin B1 helical assembly

EntireName: Endophilin B1 helical assembly
Components
  • Complex: Endophilin B1 helical assembly
    • Protein or peptide: Endophilin-B1

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Supramolecule #1: Endophilin B1 helical assembly

SupramoleculeName: Endophilin B1 helical assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Endohilin B1 N-BAR domain
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: 44 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.843246 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8.1
GridModel: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Average electron dose: 30.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 18.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 66.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12300
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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