+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19608 | |||||||||
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Title | Sulfolobus acidocaldarius threads (0406) filament. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cell surface appendage / N-glycosylation / O-glycosylation / PROTEIN FIBRIL | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Isupov MN / Gaines M / McLaren M / Daum B | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: To Be Published Title: Sulfolobus acidocaldarius threads (0406) filament. Authors: Isupov MN / Gaines M / McLaren M / Daum B | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19608.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-19608-v30.xml emd-19608.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19608_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_19608.png | 45.4 KB | ||
Filedesc metadata | emd-19608.cif.gz | 5.1 KB | ||
Others | emd_19608_half_map_1.map.gz emd_19608_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19608 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19608 | HTTPS FTP |
-Validation report
Summary document | emd_19608_validation.pdf.gz | 799.3 KB | Display | EMDB validaton report |
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Full document | emd_19608_full_validation.pdf.gz | 798.8 KB | Display | |
Data in XML | emd_19608_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_19608_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19608 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19608 | HTTPS FTP |
-Related structure data
Related structure data | 8rzlMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19608.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19608_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19608_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Filament 0406
Entire | Name: Filament 0406 |
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Components |
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-Supramolecule #1: Filament 0406
Supramolecule | Name: Filament 0406 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
-Macromolecule #1: Sulfolobus acidocaldarius threads (0406) filament.
Macromolecule | Name: Sulfolobus acidocaldarius threads (0406) filament. / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
Molecular weight | Theoretical: 19.720252 KDa |
Sequence | String: DVIYYYQGQI TVGNVAPPMY FAIQPNGNAK IGNNSNVPSY INAQPSSGGS GFTAQVNITN ATYNYYFNFM GLAVSKTGYI YLAKVAYSY TATNNPIQNA TLYIMNQQGQ IVYKYKLIVN GVVNSTLPST PLQINSGSYI VSLLIVPYQG TLPKTPSNDL A TITVNFGF SPMTASPPPI PLPSP UniProtKB: Uncharacterized protein |
-Macromolecule #3: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-MAN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 20579 / Average exposure time: 2.57 sec. / Average electron dose: 43.3 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: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8rzl: |
-Atomic model buiding 2
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8rzl: |