+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28774 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Consensus Map of the Dsl1:Qb:Qc Complex | |||||||||
Map data | Sharpened map, Consensus Map, of the Dsl1:Qb:Qc complex | |||||||||
Sample |
| |||||||||
Keywords | Tether / SNARE / Complex / TRANSPORT PROTEIN | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||
Authors | DAmico KA / Jeffrey PD / Hughson FM | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28774.map.gz | 229.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28774-v30.xml emd-28774.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28774_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_28774.png | 60.7 KB | ||
Masks | emd_28774_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-28774.cif.gz | 4.8 KB | ||
Others | emd_28774_additional_1.map.gz emd_28774_half_map_1.map.gz emd_28774_half_map_2.map.gz | 120.3 MB 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28774 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28774 | HTTPS FTP |
-Validation report
Summary document | emd_28774_validation.pdf.gz | 945.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28774_full_validation.pdf.gz | 944.6 KB | Display | |
Data in XML | emd_28774_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_28774_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28774 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28774 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_28774.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map, Consensus Map, of the Dsl1:Qb:Qc complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.114 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_28774_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened map, Consensus Map, of the Dsl1:Qb:Qc complex
File | emd_28774_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map, Consensus Map, of the Dsl1:Qb:Qc complex | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map B, Consensus Map, of the Dsl1:Qb:Qc complex
File | emd_28774_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map B, Consensus Map, of the Dsl1:Qb:Qc complex | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A, Consensus Map, of the Dsl1:Qb:Qc complex
File | emd_28774_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A, Consensus Map, of the Dsl1:Qb:Qc complex | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Dsl1 complex bound to SNARE proteins Sec20 and Use1
Entire | Name: Dsl1 complex bound to SNARE proteins Sec20 and Use1 |
---|---|
Components |
|
-Supramolecule #1: Dsl1 complex bound to SNARE proteins Sec20 and Use1
Supramolecule | Name: 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 weight | Theoretical: 255.41261 KDa |
-Supramolecule #2: Dsl1 Complex
Supramolecule | Name: Dsl1 Complex / type: complex / ID: 2 / Parent: 1 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
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. | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 | |||||||||||||||
Vitrification | Cryogen 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. | |||||||||||||||
Details | Sample was consistently in the thickest regions of ice only, often close to the edges of the carbon hole |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |