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Yorodumi- EMDB-18308: Helical reconstruction of yeast eisosome protein Pil1 bound to me... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18308 | |||||||||||||||
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Title | Helical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture -PIP2/+sterol (DOPC, DOPE, DOPS, cholesterol 30:20:20:30) | |||||||||||||||
Map data | Helical map Type II -PIP2/ sterol (D1, rise=5.04, twist=-136.50) | |||||||||||||||
Sample |
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Keywords | BAR domain / lipid reconstitution / membrane microdomain / LIPID BINDING PROTEIN | |||||||||||||||
Function / homology | Function and homology information protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / lipid droplet / cell periphery / protein localization / endocytosis / mitochondrial outer membrane / lipid binding ...protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / lipid droplet / cell periphery / protein localization / endocytosis / mitochondrial outer membrane / lipid binding / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||||||||
Authors | Kefauver JM / Zou L / Desfosses A / Loewith RJ | |||||||||||||||
Funding support | European Union, Switzerland, 4 items
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Citation | Journal: To Be Published Title: CryoEM architecture of a native stretch-sensitive membrane microdomain Authors: Kefauver JM / Hakala M / Zou L / Alba J / Espadas Moreno J / Tettamanti MG / Estrozi L / Vanni S / Roux A / Desfosses A / Loewith R | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18308.map.gz | 944.7 MB | EMDB map data format | |
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Header (meta data) | emd-18308-v30.xml emd-18308.xml | 23.2 KB 23.2 KB | Display Display | EMDB header |
Images | emd_18308.png | 206.2 KB | ||
Masks | emd_18308_msk_1.map | 1000 MB | Mask map | |
Filedesc metadata | emd-18308.cif.gz | 6.4 KB | ||
Others | emd_18308_additional_1.map.gz emd_18308_additional_2.map.gz emd_18308_additional_3.map.gz emd_18308_half_map_1.map.gz emd_18308_half_map_2.map.gz | 494.1 MB 495.1 MB 494.5 MB 928.8 MB 928.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18308 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18308 | HTTPS FTP |
-Validation report
Summary document | emd_18308_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_18308_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_18308_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_18308_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18308 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18308 | HTTPS FTP |
-Related structure data
Related structure data | 8qb9MC 8qb7C 8qb8C 8qbbC 8qbdC 8qbeC 8qbfC 8qbgC 8r1lC 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_18308.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Helical map Type II -PIP2/ sterol (D1, rise=5.04, twist=-136.50) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18308_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Helical map Type I -PIP2/ sterol (D2, rise=9.76, twist=131.91)
File | emd_18308_additional_1.map | ||||||||||||
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Annotation | Helical map Type I -PIP2/ sterol (D2, rise=9.76, twist=131.91) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Helical map Type II -PIP2/ sterol - unsharpened map
File | emd_18308_additional_2.map | ||||||||||||
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Annotation | Helical map Type II -PIP2/ sterol - unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Helical map Type III -PIP2/ sterol (D7, rise=36.54, twist=-14.47)
File | emd_18308_additional_3.map | ||||||||||||
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Annotation | Helical map Type III -PIP2/ sterol (D7, rise=36.54, twist=-14.47) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Helical map Type II -PIP2/ sterol - half map A
File | emd_18308_half_map_1.map | ||||||||||||
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Annotation | Helical map Type II -PIP2/ sterol - half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Helical map Type II -PIP2/ sterol - half map B
File | emd_18308_half_map_2.map | ||||||||||||
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Annotation | Helical map Type II -PIP2/ sterol - half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helical assembly of recombinant Pil1 protein tubulating -PIP2/+st...
Entire | Name: Helical assembly of recombinant Pil1 protein tubulating -PIP2/+sterol lipid mixture (DOPC,DOPE,DOPS,cholesterol 30:20:20:30) |
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Components |
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-Supramolecule #1: Helical assembly of recombinant Pil1 protein tubulating -PIP2/+st...
Supramolecule | Name: Helical assembly of recombinant Pil1 protein tubulating -PIP2/+sterol lipid mixture (DOPC,DOPE,DOPS,cholesterol 30:20:20:30) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50 |
-Macromolecule #1: Sphingolipid long chain base-responsive protein PIL1
Macromolecule | Name: Sphingolipid long chain base-responsive protein PIL1 / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50 |
Molecular weight | Theoretical: 38.393043 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MHRTYSLRNS RAPTASQLQN PPPPPSTTKG RFFGKGGLAY SFRRSAAGAF GPELSRKLSQ LVKIEKNVLR SMELTANERR DAAKQLSIW GLENDDDVSD ITDKLGVLIY EVSELDDQFI DRYDQYRLTL KSIRDIEGSV QPSRDRKDKI TDKIAYLKYK D PQSPKIEV ...String: MHRTYSLRNS RAPTASQLQN PPPPPSTTKG RFFGKGGLAY SFRRSAAGAF GPELSRKLSQ LVKIEKNVLR SMELTANERR DAAKQLSIW GLENDDDVSD ITDKLGVLIY EVSELDDQFI DRYDQYRLTL KSIRDIEGSV QPSRDRKDKI TDKIAYLKYK D PQSPKIEV LEQELVRAEA ESLVAEAQLS NITRSKLRAA FNYQFDSIIE HSEKIALIAG YGKALLELLD DSPVTPGETR PA YDGYEAS KQIIIDAESA LNEWTLDSAQ VKPTLSFKQD YEDFEPEEGE EEEEEDGQGR WSEDEQEDGQ IEEPEQEEEG AVE EHEQVG HQQSESLPQQ TTA UniProtKB: Sphingolipid long chain base-responsive protein PIL1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 / Details: 20mM HEPES, pH 7.4, 150mM KoAc, 2mM MgAc |
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 1.8 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 5.044 Å Applied symmetry - Helical parameters - Δ&Phi: -136.5 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 176005 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.1.2) |