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Open data
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Basic information
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Title | Native eisosome lattice bound to plasma membrane microdomain | |||||||||||||||
![]() | Native eisosome lattice - sharpened map | |||||||||||||||
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![]() | BAR domain / plasma membrane microdomain / membrane curvature / native biochemistry / LIPID BINDING PROTEIN | |||||||||||||||
Function / homology | ![]() protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / lipid droplet / cell periphery / negative regulation of protein kinase activity / protein localization / endocytosis / response to heat ...protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / lipid droplet / cell periphery / negative regulation of protein kinase activity / protein localization / endocytosis / response to heat / mitochondrial outer membrane / lipid binding / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
![]() | Kefauver JM / Zou L / Loewith RJ / Defosses A | |||||||||||||||
Funding support | European Union, ![]()
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![]() | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / ![]() ![]() ![]() Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 40.6 KB 40.6 KB | Display Display | ![]() |
Images | ![]() | 134.8 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 31.8 MB 271.1 MB 59.8 MB 267.4 MB 272.9 MB 273.9 MB 274.1 MB 272.7 MB 271.2 MB 272 MB 266.6 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 864.7 KB | Display | ![]() |
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Full document | ![]() | 864.3 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qb7MC ![]() 8qb8MC ![]() 8qb9C ![]() 8qbbC ![]() 8qbdC ![]() 8qbeC ![]() 8qbfC ![]() 8qbgC ![]() 8r1lC 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 | Native eisosome lattice - sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.327 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Additional map: Native eisosome lattice - unsharpened map
+Additional map: Native eisosome helical map (C2, rise=11.00, twist=54.02)
+Additional map: Native eisosome lattice - deepEMhancer sharpened map
+Additional map: Native eisosome helical map (C4, rise=21.27, twist=50.99)
+Additional map: Native eisosome helical map (C7, rise=37.28, twist=36.72)
+Additional map: Native eisosome helical map (C1, rise=5.58, twist=53.51)
+Additional map: Native eisosome helical map (C1, rise=5.13, twist=49.32)
+Additional map: Native eisosome helical map (C1, rise=5.2, twist=136.56)
+Additional map: Native eisosome helical map (C2, rise=10.02, twist=47.98)
+Additional map: Native eisosome helical map (C1, rise=4.89, twist=46.59)
+Additional map: Native eisosome helical map (C8, rise=37.41, twist=57.83)
+Half map: Native eisosome lattice - half map B
+Half map: Native eisosome lattice - half map A
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Sample components
-Entire : Helical lattice of native Pil1/Lsp1 protein bound to plasma membr...
Entire | Name: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain |
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Components |
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-Supramolecule #1: Helical lattice of native Pil1/Lsp1 protein bound to plasma membr...
Supramolecule | Name: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 38.393043 KDa |
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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![]() | single particle reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 7 / Details: 50mM PIPES pH 7, 300mM NaCl, 1mM CHAPS, 0.5mM DTT |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k 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: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Cylindrical map |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 2423944 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2) |