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Open data
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Basic information
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Title | Endophilin B1 dimer bound to nanodisc edge | |||||||||
![]() | Endophilin B1 dimer bound to the edge of nanodiscs | |||||||||
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![]() | BAR / N-BAR / endophilin / membrane / curvature / cardiolipin / MSP2N2 / nanodisc / peripheral membrane protein / APOPTOSIS | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Thorlacius A / Sundborger-Lunna A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Endophilin B1 dimer bound to nanodisc edge Authors: Thorlacius A / Sundborger-Lunna A | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 21.9 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 771.8 KB | Display | ![]() |
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Full document | ![]() | 771.4 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9g2wMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Endophilin B1 dimer bound to the edge of nanodiscs | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
File | emd_50986_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Endophilin B1 dimers bound to a nanodisc
Entire | Name: Endophilin B1 dimers bound to a nanodisc |
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Components |
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-Supramolecule #1: Endophilin B1 dimers bound to a nanodisc
Supramolecule | Name: Endophilin B1 dimers bound to a nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Endophilin-B1
Macromolecule | Name: Endophilin-B1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.843246 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA, pH 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 11-252 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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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. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-9g2w: |