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- EMDB-28768: Sec39:Use1:Sec20:Tip20 Local Refinement of the Dsl1:Qb:Qc Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28768
TitleSec39:Use1:Sec20:Tip20 Local Refinement of the Dsl1:Qb:Qc Complex
Map dataSharpened map, Local Refinement #3, of the Dsl1:Qb:Qc complex
Sample
  • Complex: Dsl1 complex bound to SNARE proteins Sec20 and Use1
    • Complex: Dsl1 Complex
KeywordsTether / SNARE / Complex / TRANSPORT PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsDAmico KA / Jeffrey PD / Hughson FM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007388 United States
CitationJournal: TO BE PUBLISHED
Title: CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1
Authors: DAmico KA / Stanton AE / Shirkey JD / Jeffrey PD / Hughson FM
History
DepositionNov 3, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28768.png

Downloads & links

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Map

FileDownload / File: emd_28768.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map, Local Refinement #3, of the Dsl1:Qb:Qc complex
Voxel sizeX=Y=Z: 1.114 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.6738735 - 1.0751058
Average (Standard dev.)0.00023535299 (±0.018340178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 445.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28768_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map, Local Refinement #3, of the Dsl1:Qb:Qc complex

Fileemd_28768_additional_1.map
AnnotationUnsharpened map, Local Refinement #3, of the Dsl1:Qb:Qc complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B, Local Refinement #3, of the Dsl1:Qb:Qc complex

Fileemd_28768_half_map_1.map
AnnotationHalf map B, Local Refinement #3, of the Dsl1:Qb:Qc complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A, Local Refinement #3, of the Dsl1:Qb:Qc complex

Fileemd_28768_half_map_2.map
AnnotationHalf map A, Local Refinement #3, of the Dsl1:Qb:Qc complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dsl1 complex bound to SNARE proteins Sec20 and Use1

EntireName: Dsl1 complex bound to SNARE proteins Sec20 and Use1
Components
  • Complex: Dsl1 complex bound to SNARE proteins Sec20 and Use1
    • Complex: Dsl1 Complex

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Supramolecule #1: Dsl1 complex bound to SNARE proteins Sec20 and Use1

SupramoleculeName: Dsl1 complex bound to SNARE proteins Sec20 and Use1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c
Molecular weightTheoretical: 255.41261 KDa

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Supramolecule #2: Dsl1 Complex

SupramoleculeName: Dsl1 Complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC8H18N2O4SHEPES
1.0 mMC4H10O2S2DTT
0.05 %H(C2H4O)nO(C6H4)C9H19NP40

Details: Buffer was made fresh from concentrated components and sterile filtered. NP40 was not present during protein purification but was an additive during the grid preparation.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Force=0 Wait Time=0 Blot Time=6s Drain Time=0.
DetailsSample was consistently in the thickest regions of ice only, often close to the edges of the carbon hole

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 5857 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 469193
Details: Particles were template-picked utilizing a low-resolution density map of the complex, generated from an initial subset of the data.
Startup modelType of model: NONE
Details: EM density was built without a reference model, and was generated only from refining classes of selected particles
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot (ver. 0.8.9.1) / Number images used: 49947
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 13070 / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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