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- PDB-8qb8: Lsp1 in native eisosome lattice bound to plasma membrane microdomain -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qb8 | |||||||||||||||
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Title | Lsp1 in native eisosome lattice bound to plasma membrane microdomain | |||||||||||||||
![]() | Sphingolipid long chain base-responsive protein LSP1 | |||||||||||||||
![]() | LIPID BINDING PROTEIN / BAR domain / plasma membrane microdomain / membrane curvature / native biochemistry | |||||||||||||||
Function / homology | ![]() eisosome filament / eisosome assembly / eisosome / cell periphery / negative regulation of protein kinase activity / endocytosis / response to heat / mitochondrial outer membrane / lipid binding / mitochondrion ...eisosome filament / eisosome assembly / eisosome / cell periphery / negative regulation of protein kinase activity / endocytosis / response to heat / mitochondrial outer membrane / lipid binding / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
![]() | Kefauver, J.M. / Zou, L. / Loewith, R.J. / Defosses, A. | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: CryoEM architecture of a native stretch-sensitive membrane microdomain Authors: Kefauver, J.M. / Hakala, M. / Zou, L. / Alba, J. / Espadas Moreno, J. / Tettamanti, M.G. / Estrozi, L. / Vanni, S. / Roux, A. / Desfosses, A. / Loewith, R. #1: 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 883.2 KB | Display | ![]() |
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PDB format | ![]() | 593.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 103.4 KB | Display | |
Data in CIF | ![]() | 139.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18307MC ![]() 8qb7C ![]() 8qb9C ![]() 8qbbC ![]() 8qbdC ![]() 8qbeC ![]() 8qbfC ![]() 8qbgC ![]() 8r1lC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 1 - 271 / Label seq-ID: 1 - 271
NCS oper:
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Components
#1: Protein | Mass: 38116.039 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 / Details: 50mM PIPES pH 7, 300mM NaCl, 1mM CHAPS, 0.5mM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon |
Vitrification | Cryogen name: ETHANE |
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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 defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2423944 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Accession code: P53252 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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