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- EMDB-29893: Computationally designed strut_C6_21 de novo protein assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-29893
TitleComputationally designed strut_C6_21 de novo protein assembly
Map datacryoEM map of computationally designed de novo strut_C6_21 protein
Sample
  • Complex: strut_C6_21
Keywordscomputationally designed / de novo protein / BIOSYNTHETIC PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.12 Å
AuthorsCourbet A / Huddy TF / Hsia Y
Funding support United States, 3 items
OrganizationGrant numberCountry
Other private United States
Other governmentS10OD032290 United States
Other governmentP30 CA015704-40 United States
CitationJournal: To Be Published
Title: Geometrically programmable nanomaterial construction using regularized protein building blocks
Authors: Courbet A / Huddy TF / Hsia Y
History
DepositionFeb 22, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29893.png

Downloads & links

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Map

FileDownload / File: emd_29893.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map of computationally designed de novo strut_C6_21 protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 450 pix.
= 397.35 Å		0.88 Å/pix.
x 450 pix.
= 397.35 Å		0.88 Å/pix.
x 450 pix.
= 397.35 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.883 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-0.1435506 - 0.47270033
Average (Standard dev.)0.0006983751 (±0.015886018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 397.35 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29893_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of computationally designed de novo strut C6 21 protein

Fileemd_29893_half_map_1.map
Annotationhalf map A of computationally designed de novo strut_C6_21 protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of computationally designed de novo strut C6 21 protein

Fileemd_29893_half_map_2.map
Annotationhalf map B of computationally designed de novo strut_C6_21 protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : strut_C6_21

EntireName: strut_C6_21
Components
  • Complex: strut_C6_21

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Supramolecule #1: strut_C6_21

SupramoleculeName: strut_C6_21 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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

Concentration10 mg/mL
BufferpH: 8.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
25.0 mMTrisTris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1116 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 31 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.1.2) / Number images used: 37105
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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