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- EMDB-18309: Helical reconstruction of yeast eisosome protein Pil1 bound to me... -

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Basic information

Entry
Database: EMDB / ID: EMD-18309
TitleHelical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/-sterol (DOPC, DOPE, DOPS, PI(4,5)P2 50:20:20:10)
Map dataSharpened helical map Type c plusPIP2/-sterol (D3, rise=14.55, twist=-83.25)
Sample
  • Complex: Helical assembly of recombinant Pil1 protein tubulating +PIP2/-sterol lipid mixture (DOPC,DOPE,DOPS,PI(4,5)P2 50:20:20:10)
    • Protein or peptide: Sphingolipid long chain base-responsive protein PIL1
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
KeywordsBAR 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
Eisosome component PIL1/LSP1 / Eisosome component PIL1 / AH/BAR domain superfamily
Similarity search - Domain/homology
Sphingolipid long chain base-responsive protein PIL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsKefauver JM / Zou L / Desfosses A / Loewith RJ
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission101026765European Union
European Research Council (ERC)AdG TENDOEuropean Union
Swiss National Science FoundationCRSII5_189996 Switzerland
Swiss National Science Foundation310030_207754 Switzerland
CitationJournal: 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
DepositionAug 24, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18309.png

Downloads & links

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Map

FileDownload / File: emd_18309.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened helical map Type c plusPIP2/-sterol (D3, rise=14.55, twist=-83.25)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.13308172 - 0.2541855
Average (Standard dev.)0.0005284506 (±0.012177983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18309_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map Type d plusPIP2/-sterol (D1, rise=5.078,...

Fileemd_18309_additional_1.map
AnnotationUnsharpened helical map Type d plusPIP2/-sterol (D1, rise=5.078, twist=-136.523)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map Type b plusPIP2/-sterol (D1, rise=5.420,...

Fileemd_18309_additional_2.map
AnnotationUnsharpened helical map Type b plusPIP2/-sterol (D1, rise=5.420, twist=133.600)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map Type a plusPIP2/-sterol (D4, rise=21.004,...

Fileemd_18309_additional_3.map
AnnotationUnsharpened helical map Type a plusPIP2/-sterol (D4, rise=21.004, twist=39.094)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map Type e plusPIP2/-sterol (D1, rise=4.714,...

Fileemd_18309_additional_4.map
AnnotationUnsharpened helical map Type e plusPIP2/-sterol (D1, rise=4.714, twist=-81.141)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map Type c plusPIP2/-sterol (D3, rise=14.55,...

Fileemd_18309_additional_5.map
AnnotationUnsharpened helical map Type c plusPIP2/-sterol (D3, rise=14.55, twist=-83.25)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Helical map Type c plusPIP2/-sterol - half map A

Fileemd_18309_half_map_1.map
AnnotationHelical map Type c plusPIP2/-sterol - half map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Helical map Type c plusPIP2/-sterol - half map B

Fileemd_18309_half_map_2.map
AnnotationHelical map Type c plusPIP2/-sterol - half map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of recombinant Pil1 protein tubulating +PIP2/-st...

EntireName: Helical assembly of recombinant Pil1 protein tubulating +PIP2/-sterol lipid mixture (DOPC,DOPE,DOPS,PI(4,5)P2 50:20:20:10)
Components
  • Complex: Helical assembly of recombinant Pil1 protein tubulating +PIP2/-sterol lipid mixture (DOPC,DOPE,DOPS,PI(4,5)P2 50:20:20:10)
    • Protein or peptide: Sphingolipid long chain base-responsive protein PIL1
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

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Supramolecule #1: Helical assembly of recombinant Pil1 protein tubulating +PIP2/-st...

SupramoleculeName: Helical assembly of recombinant Pil1 protein tubulating +PIP2/-sterol lipid mixture (DOPC,DOPE,DOPS,PI(4,5)P2 50:20:20:10)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50

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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
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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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Macromolecule #2: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

MacromoleculeName: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 14 / Formula: I3P
Molecular weightTheoretical: 420.096 Da
Chemical component information

ChemComp-I3P:
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4 / Details: 20 mM HEPES, pH 7.4, 150 mM KoAc, 2 mM MgAc
GridModel: EMS Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.547 Å
Applied symmetry - Helical parameters - Δ&Phi: -83.25 °
Applied symmetry - Helical parameters - Axial symmetry: D3 (2x3 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85456
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

3252


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

PDB-8qbb:
Helical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/-sterol (DOPC, DOPE, DOPS, PI(4,5)P2 50:20:20:10)

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