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- EMDB-14740: Ligand bound state of a brocolli-pepper aptamer FRET tile -

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Basic information

Entry
Database: EMDB / ID: EMD-14740
TitleLigand bound state of a brocolli-pepper aptamer FRET tile
Map dataMap sharpened with b-factor of 160
Sample
  • Complex: Ligand bound state of a brocolli-pepper aptamer FRET tile
    • RNA: brocolli-pepper aptamer
  • Ligand: 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]thiophen-2-yl]ethenyl]benzenecarbonitrile
  • Ligand: 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol
  • Ligand: POTASSIUM IONPotassium
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 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: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Tristan Ian Croll /
Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Rea-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD
#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-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14740.png

Downloads & links

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Map

FileDownload / File: emd_14740.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened with 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: 0.14
Minimum - Maximum-0.24302302 - 0.7123579
Average (Standard dev.)0.0006073777 (±0.018451815)
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_14740_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_14740_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_14740_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_14740_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Ligand bound state of a brocolli-pepper aptamer FRET tile

EntireName: Ligand bound state of a brocolli-pepper aptamer FRET tile
Components
  • Complex: Ligand bound state of a brocolli-pepper aptamer FRET tile
    • RNA: brocolli-pepper aptamer
  • Ligand: 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]thiophen-2-yl]ethenyl]benzenecarbonitrile
  • Ligand: 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol
  • Ligand: POTASSIUM IONPotassium

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

SupramoleculeName: Ligand bound state of a brocolli-pepper aptamer FRET tile
type: complex / ID: 1 / Chimera: Yes / 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: 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]...

MacromoleculeName: 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]thiophen-2-yl]ethenyl]benzenecarbonitrile
type: ligand / ID: 2 / Number of copies: 1 / Formula: J93
Molecular weightTheoretical: 365.472 Da
Chemical component information

ChemComp-J93:
4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]thiophen-2-yl]ethenyl]benzenecarbonitrile

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Macromolecule #3: 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol

MacromoleculeName: 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol
type: ligand / ID: 3 / Number of copies: 1 / Formula: 1TU
Molecular weightTheoretical: 254.233 Da
Chemical component information

ChemComp-1TU:
4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / 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.
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.00045000000000000004 kPa / Details: 15mA of current.
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
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: 5354 / Average electron dose: 60.0 e/Å2
Details: Collected with a calibrated pixel size of 0.647 Angstrom
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 729630
Details: Picked from templates generated from an ab initio model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 5 / Avg.num./class: 75000 / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3)
Details: Local refinement was performed using a mask covering the entire volume.
Number images used: 150204
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

7ptq

,

7eop

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7zj4:
Ligand bound state of a brocolli-pepper aptamer FRET tile

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