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- EMDB-19822: Helical reconstruction of yeast eisosome protein Pil1 bound to me... -

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Basic information

Entry
Database: EMDB / ID: EMD-19822
TitleHelical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/+bromosterol (DOPC, DOPE, DOPS, bromo-ergosterol, PI(4,5)P2 35:20:20:15:10)
Map dataSharpened helical map 2b PIP2/ bromosterol (D1, rise 5.338, twist 133.559)
Sample
  • Complex: Helical assembly of recombinant Pil1 protein tubulating +PIP2/+bromosterol lipid mixture (DOPC, DOPE, DOPS, bromo-ergosterol, PI(4,5)P2 35:20:20:15:10)
    • Protein or peptide: Sphingolipid long chain base-responsive protein PIL1
KeywordsBAR domain / lipid reconstitution / membrane microdomain / LIPID BINDING PROTEIN
Function / homologyEisosome component PIL1/LSP1 / Eisosome component PIL1 / AH/BAR domain superfamily / Sphingolipid long chain base-responsive protein PIL1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsKefauver JM / Zou L / Desfosses A / Loewith RJ
Funding supportEuropean Union, Switzerland, 3 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission101026765European Union
European Research Council (ERC)AdG TENDOEuropean Union
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
DepositionMar 10, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19822.png

Downloads & links

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Map

FileDownload / File: emd_19822.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened helical map 2b PIP2/ bromosterol (D1, rise 5.338, twist 133.559)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 300 pix.
= 402. Å		1.34 Å/pix.
x 300 pix.
= 402. Å		1.34 Å/pix.
x 300 pix.
= 402. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.0.71210.71210.7121
CCP4 map header1.341.341.34
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.13557693 - 0.2578498
Average (Standard dev.)0.0017403599 (±0.0141342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions760760760
Spacing760760760
CellA=B=C: 541.19604 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19822_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unsharpened helical map 2b PIP2/ bromosterol (D1, rise...

Fileemd_19822_additional_1.map
AnnotationUnsharpened helical map 2b PIP2/ bromosterol (D1, rise 5.338, twist 133.559)
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map 1b PIP2/ bromosterol (D4, rise...

Fileemd_19822_additional_2.map
AnnotationUnsharpened helical map 1b PIP2/ bromosterol (D4, rise 20.64, twist 219.047)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map 8b PIP2/ bromosterol (D2, rise...

Fileemd_19822_additional_3.map
AnnotationUnsharpened helical map 8b PIP2/ bromosterol (D2, rise 11.025, twist 42.306)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened helical map 9b PIP2/ bromosterol (D1, rise...

Fileemd_19822_additional_4.map
AnnotationUnsharpened helical map 9b PIP2/ bromosterol (D1, rise 5.571, twist 152.247)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Helical map 2b PIP2/ bromosterol - half map A

Fileemd_19822_half_map_1.map
AnnotationHelical map 2b PIP2/ bromosterol - half map A
Projections & Slices
AxesZYX

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Sample components

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

EntireName: Helical assembly of recombinant Pil1 protein tubulating +PIP2/+bromosterol lipid mixture (DOPC, DOPE, DOPS, bromo-ergosterol, PI(4,5)P2 35:20:20:15:10)
Components
  • Complex: Helical assembly of recombinant Pil1 protein tubulating +PIP2/+bromosterol lipid mixture (DOPC, DOPE, DOPS, bromo-ergosterol, PI(4,5)P2 35:20:20:15:10)
    • Protein or peptide: Sphingolipid long chain base-responsive protein PIL1

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

SupramoleculeName: Helical assembly of recombinant Pil1 protein tubulating +PIP2/+bromosterol lipid mixture (DOPC, DOPE, DOPS, bromo-ergosterol, PI(4,5)P2 35:20:20:15:10)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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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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: 20mM HEPES, pH 7.4, 150mM KoAc, 2mM 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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.33 Å
Applied symmetry - Helical parameters - Δ&Phi: 133.61 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56475
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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