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- EMDB-25579: D3-C3 computationally-designed rotor -

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Basic information

Entry
Database: EMDB / ID: EMD-25579
TitleD3-C3 computationally-designed rotor
Map dataD3-C3 Computationally-designed Rotor (processed in C3)
Sample
  • Complex: D3-symmetric axel and C3-symmetric ring
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.2 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) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25579.png

Downloads & links

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Map

FileDownload / File: emd_25579.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD3-C3 Computationally-designed Rotor (processed in C3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.36 Å/pix.
x 128 pix.
= 430.08 Å		3.36 Å/pix.
x 128 pix.
= 430.08 Å		3.36 Å/pix.
x 128 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.14 / Movie #1: 5.14
Minimum - Maximum-10.756518 - 23.257158
Average (Standard dev.)0.024843035 (±0.41509074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.363.363.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
start NX/NY/NZ154162115
NX/NY/NZ9384171
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-10.75723.2570.025

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Supplemental data

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Additional map: D3-C3 Computationally-designed Rotor (processed in D3)

Fileemd_25579_additional_1.map
AnnotationD3-C3 Computationally-designed Rotor (processed in D3)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: D3-C3 Computationally-designed Rotor (processed in C1)

Fileemd_25579_additional_2.map
AnnotationD3-C3 Computationally-designed Rotor (processed in C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : D3-symmetric axel and C3-symmetric ring

EntireName: D3-symmetric axel and C3-symmetric ring
Components
  • Complex: D3-symmetric axel and C3-symmetric ring

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Supramolecule #1: D3-symmetric axel and C3-symmetric ring

SupramoleculeName: D3-symmetric axel and C3-symmetric ring / type: complex / ID: 1 / Parent: 0
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: 8.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 79.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16244
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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