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- EMDB-18307: Native eisosome lattice bound to plasma membrane microdomain -

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Basic information

Entry
Database: EMDB / ID: EMD-18307
TitleNative eisosome lattice bound to plasma membrane microdomain
Map dataNative eisosome lattice - sharpened map
Sample
  • Complex: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain
    • Protein or peptide: Sphingolipid long chain base-responsive protein PIL1
KeywordsBAR domain / plasma membrane microdomain / membrane curvature / native biochemistry / LIPID BINDING PROTEIN
Function / homology
Function and homology information


protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / membrane organization / lipid droplet / cell periphery / endocytosis / intracellular protein localization / response to heat ...protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / membrane organization / lipid droplet / cell periphery / endocytosis / intracellular protein localization / response to heat / mitochondrial outer membrane / lipid binding / mitochondrion / plasma membrane / cytoplasm
Similarity search - Function
Eisosome component PIL1/LSP1 / Eisosome component PIL1 / AH/BAR domain superfamily
Similarity search - Domain/homology
Sphingolipid long chain base-responsive protein PIL1 / Sphingolipid long chain base-responsive protein LSP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKefauver JM / Zou L / Loewith RJ / Desfosses A
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionIF-2020-101026765-MEMTOREuropean Union
European Research Council (ERC)AdG TENDOEuropean Union
Swiss National Science FoundationCRSII5_189996 METEORIC Switzerland
Swiss National Science Foundation310030_207754 Switzerland
CitationJournal: 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
DepositionAug 24, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18307.png

Downloads & links

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Map

FileDownload / File: emd_18307.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative eisosome lattice - sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 339.712 Å		1.33 Å/pix.
x 256 pix.
= 339.712 Å		1.33 Å/pix.
x 256 pix.
= 339.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.327 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-3.8135464 - 5.48576
Average (Standard dev.)0.01581569 (±0.13591683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Native eisosome lattice - unsharpened map

Fileemd_18307_additional_1.map
AnnotationNative eisosome lattice - unsharpened map
Projections & Slices
AxesZYX

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Additional map: Native eisosome helical map (C2, rise=11.00, twist=54.02)

Fileemd_18307_additional_10.map
AnnotationNative eisosome helical map (C2, rise=11.00, twist=54.02)
Projections & Slices
AxesZYX

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Additional map: Native eisosome lattice - deepEMhancer sharpened map

Fileemd_18307_additional_11.map
AnnotationNative eisosome lattice - deepEMhancer sharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C4, rise=21.27, twist=50.99)

Fileemd_18307_additional_2.map
AnnotationNative eisosome helical map (C4, rise=21.27, twist=50.99)
Projections & Slices
AxesZYX

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Additional map: Native eisosome helical map (C7, rise=37.28, twist=36.72)

Fileemd_18307_additional_3.map
AnnotationNative eisosome helical map (C7, rise=37.28, twist=36.72)
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C1, rise=5.58, twist=53.51)

Fileemd_18307_additional_4.map
AnnotationNative eisosome helical map (C1, rise=5.58, twist=53.51)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C1, rise=5.13, twist=49.32)

Fileemd_18307_additional_5.map
AnnotationNative eisosome helical map (C1, rise=5.13, twist=49.32)
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C1, rise=5.2, twist=136.56)

Fileemd_18307_additional_6.map
AnnotationNative eisosome helical map (C1, rise=5.2, twist=136.56)
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C2, rise=10.02, twist=47.98)

Fileemd_18307_additional_7.map
AnnotationNative eisosome helical map (C2, rise=10.02, twist=47.98)
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C1, rise=4.89, twist=46.59)

Fileemd_18307_additional_8.map
AnnotationNative eisosome helical map (C1, rise=4.89, twist=46.59)
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Native eisosome helical map (C8, rise=37.41, twist=57.83)

Fileemd_18307_additional_9.map
AnnotationNative eisosome helical map (C8, rise=37.41, twist=57.83)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Native eisosome lattice - half map B

Fileemd_18307_half_map_1.map
AnnotationNative eisosome lattice - half map B
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Native eisosome lattice - half map A

Fileemd_18307_half_map_2.map
AnnotationNative eisosome lattice - half map A
Projections & Slices
AxesZYX

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Sample components

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Entire : Helical lattice of native Pil1/Lsp1 protein bound to plasma membr...

EntireName: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain
Components
  • Complex: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain
    • Protein or peptide: Sphingolipid long chain base-responsive protein PIL1

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Supramolecule #1: Helical lattice of native Pil1/Lsp1 protein bound to plasma membr...

SupramoleculeName: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50 / Organelle: eisosome / Location in cell: plasma membrane

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Macromolecule #1: Sphingolipid long chain base-responsive protein PIL1

MacromoleculeName: Sphingolipid long chain base-responsive protein PIL1 / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50
Molecular weightTheoretical: 38.393043 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7 / Details: 50mM PIPES pH 7, 300mM NaCl, 1mM CHAPS, 0.5mM DTT
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: OTHER / Details: Cylindrical map
Final reconstructionResolution.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 assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)

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Atomic model buiding 1

Initial modelPDB ID:

3252


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8qb7:
Pil1 in native eisosome lattice bound to plasma membrane microdomain

PDB-8qb8:
Lsp1 in native eisosome lattice bound to plasma membrane microdomain

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