+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50981 | |||||||||
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Title | Endophilin B1 dimers bound to nanodiscs | |||||||||
Map data | C1 consensus map of Endophilin B1 dimers bound to a nanodisc. | |||||||||
Sample |
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Keywords | BAR / N-BAR / endophilin / membrane / curvature / cardiolipin / MSP2N2 / nanodisc / peripheral membrane protein / APOPTOSIS | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
Authors | Thorlacius A / Sundborger-Lunna A | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50981.map.gz | 31.7 MB | EMDB map data format | |
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Header (meta data) | emd-50981-v30.xml emd-50981.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50981_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_50981.png | 70.5 KB | ||
Masks | emd_50981_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-50981.cif.gz | 6 KB | ||
Others | emd_50981_half_map_1.map.gz emd_50981_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50981 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50981 | HTTPS FTP |
-Validation report
Summary document | emd_50981_validation.pdf.gz | 840.1 KB | Display | EMDB validaton report |
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Full document | emd_50981_full_validation.pdf.gz | 839.6 KB | Display | |
Data in XML | emd_50981_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_50981_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50981 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50981 | HTTPS FTP |
-Related structure data
Related structure data | 9g2rMC 9g2uC 9g2wC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50981.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | C1 consensus map of Endophilin B1 dimers bound to a nanodisc. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
File | emd_50981_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50981_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50981_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Homo sapiens (human) |
-Macromolecule #1: Endophilin-B1
Macromolecule | Name: Endophilin-B1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.843246 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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: FIELD EMISSION GUN |
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 |
+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 | Experimental models determined from locally refined maps were rigid body fitted into the consensus map. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-9g2r: |