+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15026 | |||||||||
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Title | Avidin + Biotin-Tempo | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Avidin / Biotin / TEMPO free radical / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) / chicken (chicken) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.08 Å | |||||||||
Authors | Milani J / Myasnikov A / Beckert B / Nazarov S / Ansermet JP / Saenz F | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: To Be Published Title: Avidin + Biotin-Tempo Authors: Milani J / Myasnikov A / Beckert B / Nazarov S / Ansermet JP / Saenz F | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15026.map.gz | 107.6 MB | EMDB map data format | |
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Header (meta data) | emd-15026-v30.xml emd-15026.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15026_fsc.xml emd_15026_fsc_2.xml | 12.7 KB 12.7 KB | Display Display | FSC data file |
Images | emd_15026.png | 113.2 KB | ||
Masks | emd_15026_msk_1.map | 216 MB | Mask map | |
Others | emd_15026_additional_1.map.gz emd_15026_additional_2.map.gz emd_15026_half_map_1.map.gz emd_15026_half_map_2.map.gz | 203.3 MB 7.3 MB 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15026 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15026 | HTTPS FTP |
-Validation report
Summary document | emd_15026_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_15026_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_15026_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_15026_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15026 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15026 | HTTPS FTP |
-Related structure data
Related structure data | 7zylMC 7zn1C 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_15026.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.45 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15026_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_15026_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_15026_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15026_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15026_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Avidin
Entire | Name: Avidin |
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Components |
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-Supramolecule #1: Avidin
Supramolecule | Name: Avidin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Avidin
Macromolecule | Name: Avidin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: chicken (chicken) |
Molecular weight | Theoretical: 16.787193 KDa |
Sequence | String: MVHATSPLLL LLLLSLALVA PGLSARKCSL TGKWTNDLGS NMTIGAVNSR GEFTGTYITA VTATSNEIKE SPLHGTQNTI NKRTQPTFG FTVNWKFSES TTVFTGQCFI DRNGKEVLKT MWLLRSSVND IGDDWKATRV GINIFTRLRT QKE |
-Macromolecule #3: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a...
Macromolecule | Name: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide type: ligand / ID: 3 / Number of copies: 4 / Formula: KFL |
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Molecular weight | Theoretical: 412.59 Da |
Chemical component information | ChemComp-KFL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 10 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 86.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.9 µm / Calibrated magnification: 311110 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 270000 |
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 | Protocol: FLEXIBLE FIT |
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Output model | PDB-7zyl: |