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- EMDB-14741: Unbound state of a brocolli-pepper aptamer FRET tile -

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Basic information

Entry
Database: EMDB / ID: EMD-14741
TitleUnbound state of a brocolli-pepper aptamer FRET tile
Map dataMap sharpened with a b-factor of 160.
Sample
  • Complex: Unbound state of a brocolli-pepper aptamer FRET tile
    • RNA: brocolli-pepper aptamer
  • Ligand: POTASSIUM ION
KeywordsRNA / origami / aptamer / fret
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.55 Å
AuthorsMcRae EKS / Vallina NS / Hansen BK / Boussebayle A / Andersen ES
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Danish Council for Independent Research Denmark
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
DepositionApr 8, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14741.png

Downloads & links

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Map

FileDownload / File: emd_14741.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened with a b-factor of 160.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 216 pix.
= 278.64 Å		1.29 Å/pix.
x 216 pix.
= 278.64 Å		1.29 Å/pix.
x 216 pix.
= 278.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.099760376 - 0.47850803
Average (Standard dev.)0.00072419236 (±0.016878549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 278.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14741_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_14741_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_14741_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_14741_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Unbound state of a brocolli-pepper aptamer FRET tile

EntireName: Unbound state of a brocolli-pepper aptamer FRET tile
Components
  • Complex: Unbound state of a brocolli-pepper aptamer FRET tile
    • RNA: brocolli-pepper aptamer
  • Ligand: POTASSIUM ION

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Supramolecule #1: Unbound state of a brocolli-pepper aptamer FRET tile

SupramoleculeName: Unbound state of a brocolli-pepper aptamer FRET tile / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: brocolli-pepper aptamer

MacromoleculeName: brocolli-pepper aptamer / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 120.700953 KDa
SequenceString: 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

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Details: 40mM HEPES pH 7.5, 5mM MgCl2, 50mM KCl. Filtered through 0.22 um filter.
VitrificationCryogen 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..
DetailsSample was purified by size exclusion chromatography.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Particle selectionNumber selected: 478981
Details: Picked from templates generated from an ab initio model
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3)
Details: Local refinement was performed in cryoSPARC using a mask that covers the entire particle volume
Number images used: 51278
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 55000 / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7ptq

source_name: PDB, initial_model_type: experimental model

7eop

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7zj5:
Unbound state of a brocolli-pepper aptamer FRET tile.

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