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Open data
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Basic information
Entry | Database: PDB / ID: 7zj5 | ||||||
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Title | Unbound state of a brocolli-pepper aptamer FRET tile. | ||||||
![]() | brocolli-pepper aptamer | ||||||
![]() | RNA / origami / aptamer / fret | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.55 Å | ||||||
![]() | McRae, E.K.S. / Vallina, N.S. / Hansen, B.K. / Boussebayle, A. / Andersen, E.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure determination of Pepper-Broccoli FRET pair by RNA origami scaffolding Authors: McRae, E.K.S. / Vallina, N.S. / Hansen, B.K. / Boussebayle, A. / Andersen, E.S. #1: ![]() Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Afonine, P.V. / Poon, B.K. / Read, R.J. / Sobolev, O.V. / Terwilliger, T.C. / Urzhumtsev, A. / Adams, P.D. #2: ![]() Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Authors: Croll, T.I. #3: ![]() Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Authors: Punjani, A. / Rubinstein, J.L. / Fleet, D.J. / Brubaker, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14741MC ![]() 7zj4C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: RNA chain | Mass: 120700.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#2: Chemical | ChemComp-K / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Unbound state of a brocolli-pepper aptamer FRET tile / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.12 MDa / Experimental value: NO |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: synthetic construct (others) |
Buffer solution | pH: 7.5 Details: 40mM HEPES pH 7.5, 5mM MgCl2, 50mM KCl. Filtered through 0.22 um filter. |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was purified by size exclusion chromatography. |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K Details: 3 uL sample, blotted onto double layer of whatman filter paper for 6 seconds. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1605 Details: Collected with a calibrated pixel size of 0.647 Angstrom |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 478981 Details: Picked from templates generated from an ab initio model | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51278 / Algorithm: BACK PROJECTION Details: Local refinement was performed in cryoSPARC using a mask that covers the entire particle volume Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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