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Open data
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Basic information
Entry | Database: PDB / ID: 9g2u | ||||||
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Title | Endophilin B1 dimer bound to nanodisc center | ||||||
![]() | Endophilin-B1 | ||||||
![]() | APOPTOSIS / BAR / N-BAR / endophilin / membrane / curvature / cardiolipin / MSP2N2 / nanodisc / peripheral membrane protein | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
![]() | Thorlacius, A. / Sundborger-Lunna, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Endophilin B1 dimers bound to nanodiscs Authors: Thorlacius, A. / Sundborger-Lunna, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.2 KB | Display | ![]() |
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PDB format | ![]() | 70.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 50984MC ![]() 9g2rC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 40843.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Endophilin B1 dimers bound to a nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA, pH 7.4 |
Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5026978 | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273120 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | Protocol: 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 building | Accession code: AF-Q9Y371-F1-model_v4 / Chain residue range: 11-252 / Source name: AlphaFold / Type: in silico model |