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- EMDB-25575: D8-C4 computationally-designed Rotor -

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Basic information

Entry
Database: EMDB / ID: EMD-25575
TitleD8-C4 computationally-designed Rotor
Map dataD8-C4 computationally-designed rotor
Sample
  • Complex: D8-symmetric axel coupled with a C4-symmetric ring.
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsHansen JM / Courbet A / Quispe J / Kollman JM / Baker D
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1629214 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008268 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD032290 United States
CitationJournal: Science / Year: 2022
Title: Computational design of mechanically coupled axle-rotor protein assemblies.
Authors: A Courbet / J Hansen / Y Hsia / N Bethel / Y-J Park / C Xu / A Moyer / S E Boyken / G Ueda / U Nattermann / D Nagarajan / D-A Silva / W Sheffler / J Quispe / A Nord / N King / P Bradley / D ...Authors: A Courbet / J Hansen / Y Hsia / N Bethel / Y-J Park / C Xu / A Moyer / S E Boyken / G Ueda / U Nattermann / D Nagarajan / D-A Silva / W Sheffler / J Quispe / A Nord / N King / P Bradley / D Veesler / J Kollman / D Baker /
Abstract: Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of ...Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.
History
DepositionNov 29, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25575.png

Downloads & links

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Map

FileDownload / File: emd_25575.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD8-C4 computationally-designed rotor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
2.32 Å/pix.
x 200 pix.
= 464. Å		2.32 Å/pix.
x 200 pix.
= 464. Å		2.32 Å/pix.
x 200 pix.
= 464. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.35
Minimum - Maximum-10.718444 - 12.221949
Average (Standard dev.)7.7922456e-13 (±0.22162046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 464.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: D8-C4 computationally-designed rotor (focused refinement on ring component)...

Fileemd_25575_additional_1.map
AnnotationD8-C4 computationally-designed rotor (focused refinement on ring component)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: D8-C4 computationally-designed rotor (focused refinement on ring component)...

Fileemd_25575_additional_2.map
AnnotationD8-C4 computationally-designed rotor (focused refinement on ring component)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : D8-symmetric axel coupled with a C4-symmetric ring.

EntireName: D8-symmetric axel coupled with a C4-symmetric ring.
Components
  • Complex: D8-symmetric axel coupled with a C4-symmetric ring.

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Supramolecule #1: D8-symmetric axel coupled with a C4-symmetric ring.

SupramoleculeName: D8-symmetric axel coupled with a C4-symmetric ring. / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab initio
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50686
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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