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- EMDB-42921: De novo designed KWOCA 70 nanoparticle - Assembly in D2 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-42921
TitleDe novo designed KWOCA 70 nanoparticle - Assembly in D2 symmetry
Map dataMain Map
Sample
  • Complex: Designed nanoparticle KWOCA 70 - D2 assembly
Keywordsprotein design / nanoparticles / cryptic sites / degreaser / soluble expression / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsAntanasijevic A / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeOPP1196345 United States
CitationJournal: To Be Published
Title: Local structural flexibility drives oligomorphism in computationally designed protein assemblies
Authors: Khmelinskaia A / Bethel NP / Fatehi F / Antanasijevic A / Borst AJ / Lai SH / Wang JY / Mallik BB / Miranda MC / Watkins AM / Ogohara C / Caldwell S / Wu M / Heck AJR / Veesler D / Ward AB / ...Authors: Khmelinskaia A / Bethel NP / Fatehi F / Antanasijevic A / Borst AJ / Lai SH / Wang JY / Mallik BB / Miranda MC / Watkins AM / Ogohara C / Caldwell S / Wu M / Heck AJR / Veesler D / Ward AB / Baker D / Twarock R / King NP
History
DepositionNov 23, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42921.png

Downloads & links

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Map

FileDownload / File: emd_42921.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 400 pix.
= 460. Å		1.15 Å/pix.
x 400 pix.
= 460. Å		1.15 Å/pix.
x 400 pix.
= 460. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0030251963 - 0.01653802
Average (Standard dev.)0.00006857423 (±0.00082005473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 460.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42921_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_42921_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_42921_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Designed nanoparticle KWOCA 70 - D2 assembly

EntireName: Designed nanoparticle KWOCA 70 - D2 assembly
Components
  • Complex: Designed nanoparticle KWOCA 70 - D2 assembly

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Supramolecule #1: Designed nanoparticle KWOCA 70 - D2 assembly

SupramoleculeName: Designed nanoparticle KWOCA 70 - D2 assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Self-assembling nanoparticle expressed recombinantly
Source (natural)Organism: synthetic construct (others)

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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

Concentration4.58 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTris-HClTris-HCl
150.0 mMNaClSodium chloride
5.0 %GlycerolGlycerol

Details: TBS + 5% glycerol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time varied between 4 and 7 seconds..
DetailsSelf-assembling nanoparticle was expressed in bacterial cells and purified using affinity chromatography and size-exclusion chromatography.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-49 / Number grids imaged: 1 / Number real images: 2364 / Average exposure time: 9.8 sec. / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsFrames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
Particle selectionNumber selected: 413660 / Details: CryoSPARC template picker
Startup modelType of model: OTHER
Details: Map obtained from Ab initio reconstruction in cryoSPARC with application of symmetry
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: D2 symmetry applied. Mask around the protein complex
Number images used: 32790
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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