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- PDB-6up6: Endophilin B1 helical scaffold -

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Basic information

Entry
Database: PDB / ID: 6up6
TitleEndophilin B1 helical scaffold
ComponentsEndophilin-B1
KeywordsCYTOSOLIC PROTEIN / Membrane binding / amphipathic helix / BAR protein / SH3 domain / membrane trafficking / cell death
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å
AuthorsBhatt, V.S. / Sundborger-Lunna, A.C.
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
M: Endophilin-B1
N: Endophilin-B1
O: Endophilin-B1
P: Endophilin-B1
Q: Endophilin-B1
R: Endophilin-B1
S: Endophilin-B1
T: Endophilin-B1
V: Endophilin-B1
W: Endophilin-B1
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
m: Endophilin-B1
n: Endophilin-B1
o: Endophilin-B1
p: Endophilin-B1
q: Endophilin-B1
r: Endophilin-B1
s: Endophilin-B1
t: Endophilin-B1
v: Endophilin-B1
w: Endophilin-B1


Theoretical massNumber of molelcules
Total (without water)1,797,10344
Polymers1,797,10344
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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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.: 44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3GLB1, KIAA0491, CGI-61 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y371

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Endophilin B1 helical assembly / Type: COMPLEX / Details: Endohilin B1 N-BAR domain / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21DE3
Buffer solutionpH: 8.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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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 / Cs: 2.7 mm
Image recordingElectron dose: 30 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 66.6 ° / Axial rise/subunit: 18.7 Å / Axial symmetry: C1
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12300 / Symmetry type: HELICAL

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