+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14741 | |||||||||
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Title | Unbound state of a brocolli-pepper aptamer FRET tile | |||||||||
Map data | Map sharpened with a b-factor of 160. | |||||||||
Sample |
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Keywords | RNA / origami / aptamer / fret | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.55 Å | |||||||||
Authors | McRae EKS / Vallina NS / Hansen BK / Boussebayle A / Andersen ES | |||||||||
Funding support | Denmark, 1 items
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Citation | Journal: To Be Published Title: Structure determination of Pepper-Broccoli FRET pair by RNA origami scaffolding Authors: McRae EKS / Vallina NS / Hansen BK / Boussebayle A / Andersen ES #1: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD #2: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Authors: Croll TI #3: Journal: Nat Methods / Year: 2017 Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Authors: Punjani A / Rubinstein JL / Fleet DJ / Brubaker MA | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14741.map.gz | 36.3 MB | EMDB map data format | |
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Header (meta data) | emd-14741-v30.xml emd-14741.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14741_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_14741.png | 28 KB | ||
Masks | emd_14741_msk_1.map | 38.4 MB | Mask map | |
Others | emd_14741_additional_1.map.gz emd_14741_half_map_1.map.gz emd_14741_half_map_2.map.gz | 19.2 MB 35.7 MB 35.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14741 | HTTPS FTP |
-Validation report
Summary document | emd_14741_validation.pdf.gz | 902.9 KB | Display | EMDB validaton report |
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Full document | emd_14741_full_validation.pdf.gz | 902.4 KB | Display | |
Data in XML | emd_14741_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_14741_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14741 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14741 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14741.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map sharpened with a b-factor of 160. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.29 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14741_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_14741_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_14741_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_14741_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Unbound state of a brocolli-pepper aptamer FRET tile
Entire | Name: Unbound state of a brocolli-pepper aptamer FRET tile |
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Components |
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-Supramolecule #1: Unbound state of a brocolli-pepper aptamer FRET tile
Supramolecule | Name: Unbound state of a brocolli-pepper aptamer FRET tile / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 120 KDa |
-Macromolecule #1: brocolli-pepper aptamer
Macromolecule | Name: brocolli-pepper aptamer / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 120.700953 KDa |
Sequence | String: GGAUACGUCU ACGCUCAGUG ACGGACUCUC UUCGGAGAGU CUGACAUCCG AACCAUACAC GGAUGUGCCU CGCCGAACAG UCUACGGCG AGCUUAAGCG CUGGGGACGC CCAACGCAUC ACAAAGACUG AGUGAUGAAC CAGAAGUAUG GACUGGUUGC G UUGGUGGA ...String: GGAUACGUCU ACGCUCAGUG ACGGACUCUC UUCGGAGAGU CUGACAUCCG AACCAUACAC GGAUGUGCCU CGCCGAACAG UCUACGGCG AGCUUAAGCG CUGGGGACGC CCAACGCAUC ACAAAGACUG AGUGAUGAAC CAGAAGUAUG GACUGGUUGC G UUGGUGGA GACGGUCGGG UCCAGUUCGC UGUCGAGUAG AGUGUGGGCU CCAUCGACGC CGCUUUAAGG UCCCCAAUCG UG GCGUGUC GGCCUGCUUC GGCAGGCACU GGCGCCGGGA CCUUGAAGAG AUGAGAUUUC GAUCUCAUCU UUGGGUGUCU CUG GUGCUU GAGGGCCCUG UGUUCGCACA GGGCCGCUCA CUGGGUGUGG ACGUAUCC |
-Macromolecule #2: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 7.5 Details: 40mM HEPES pH 7.5, 5mM MgCl2, 50mM KCl. Filtered through 0.22 um filter. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: LEICA EM GP Details: 3 uL sample, blotted onto double layer of whatman filter paper for 6 seconds.. |
Details | Sample was purified by size exclusion chromatography. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1605 / Average electron dose: 60.0 e/Å2 Details: Collected with a calibrated pixel size of 0.647 Angstrom |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |