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- EMDB-16847: CryoEM structure of holo e4D2 -

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Basic information

Entry
Database: EMDB / ID: EMD-16847
TitleCryoEM structure of holo e4D2
Map data
Sample
  • Complex: Holo e4D2
KeywordsDe novo / Heme / Four-helix-bundle / Maquette / BIOSYNTHETIC PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsYadav KNS / Hutchins G / Berger Schaffitzel C / Anderson R
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R016445/1 United Kingdom
Wellcome Trust210701/Z/18/Z United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: An expandable, modular de novo protein platform for precision redox engineering.
Authors: George H Hutchins / Claire E M Noble / H Adrian Bunzel / Christopher Williams / Paulina Dubiel / Sathish K N Yadav / Paul M Molinaro / Rob Barringer / Hector Blackburn / Benjamin J Hardy / ...Authors: George H Hutchins / Claire E M Noble / H Adrian Bunzel / Christopher Williams / Paulina Dubiel / Sathish K N Yadav / Paul M Molinaro / Rob Barringer / Hector Blackburn / Benjamin J Hardy / Alice E Parnell / Charles Landau / Paul R Race / Thomas A A Oliver / Ronald L Koder / Matthew P Crump / Christiane Schaffitzel / A Sofia F Oliveira / Adrian J Mulholland / J L Ross Anderson /
Abstract: The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo ...The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo diheme "maquette" protein, 4D2, which we subsequently use to create an expanded, modular platform for heme protein design. A well-folded monoheme variant was created by computational redesign, which was then utilized for the experimental validation of continuum electrostatic redox potential calculations. This demonstrates how fundamental biophysical properties can be predicted and fine-tuned. 4D2 was then extended into a tetraheme helical bundle, representing a 7 nm molecular wire. Despite a molecular weight of only 24 kDa, electron cryomicroscopy illustrated a remarkable level of detail, indicating the positioning of the secondary structure and the heme cofactors. This robust, expressible, highly thermostable and readily designable modular platform presents a valuable resource for redox protein design and the future construction of artificial electron-conducting circuitry.
History
DepositionMar 14, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16847.png

Downloads & links

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Map

FileDownload / File: emd_16847.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 120 pix.
= 126. Å		1.05 Å/pix.
x 120 pix.
= 126. Å		1.05 Å/pix.
x 120 pix.
= 126. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0145
Minimum - Maximum-0.04002445 - 0.056217574
Average (Standard dev.)0.00056967785 (±0.0033357951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 125.99999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16847_msk_1.map
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Half map: #1

Fileemd_16847_half_map_1.map
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Half map: #2

Fileemd_16847_half_map_2.map
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Sample components

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Entire : Holo e4D2

EntireName: Holo e4D2
Components
  • Complex: Holo e4D2

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Supramolecule #1: Holo e4D2

SupramoleculeName: Holo e4D2 / type: complex / ID: 1 / Parent: 0
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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 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: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13303
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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