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- EMDB-28760: Dsl1:Sec39 Local Refinement of the Dsl1:Qb:Qc Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28760
TitleDsl1:Sec39 Local Refinement of the Dsl1:Qb:Qc Complex
Map dataSharpened map, Local Refinement #2, 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: 6.2 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: Nat Struct Mol Biol / Year: 2024
Title: Structure of a membrane tethering complex incorporating multiple SNAREs.
Authors: Kevin A DAmico / Abigail E Stanton / Jaden D Shirkey / Sophie M Travis / Philip D Jeffrey / Frederick M Hughson /
Abstract: Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial ...Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here we present a cryo-electron microscopy structure of the simplest known MTC, the 255-kDa Dsl1 complex of Saccharomyces cerevisiae, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine.
History
DepositionNov 3, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28760.png

Downloads & links

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Map

FileDownload / File: emd_28760.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map, Local Refinement #2, of the Dsl1:Qb:Qc complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 400 pix.
= 445.6 Å		1.11 Å/pix.
x 400 pix.
= 445.6 Å		1.11 Å/pix.
x 400 pix.
= 445.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.0982589 - 1.6577282
Average (Standard dev.)0.000035813162 (±0.020121615)
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_28760_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 #2, of the Dsl1:Qb:Qc complex

Fileemd_28760_additional_1.map
AnnotationUnsharpened map, Local Refinement #2, 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 #2, of the Dsl1:Qb:Qc complex

Fileemd_28760_half_map_1.map
AnnotationHalf map B, Local Refinement #2, 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 #2, of the Dsl1:Qb:Qc complex

Fileemd_28760_half_map_2.map
AnnotationHalf map A, Local Refinement #2, 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.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.1)
Details: correction was performed using the Patch CTF Estimation tool in CryoSPARC
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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: 6.2 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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