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

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Basic information

Entry
Database: PDB / ID: 9g2u
TitleEndophilin B1 dimer bound to nanodisc center
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 / 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 / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsThorlacius, A. / Sundborger-Lunna, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2021-05423 Sweden
CitationJournal: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endophilin-B1
B: Endophilin-B1


Theoretical massNumber of molelcules
Total (without water)81,6862
Polymers81,6862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
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.: 2
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) / References: UniProt: Q9Y371

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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
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
13Servalcatmodel refinement
14PHENIXmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5026978
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.45 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: Alphafold 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.
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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