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- EMDB-27659: cryoEM map of de novo hallucinated homooligomer of C18-C6 symmetr... -

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Basic information

Entry
Database: EMDB / ID: EMD-27659
TitlecryoEM map of de novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265.
Map dataEM map
Sample
  • Complex: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265.
    • Protein or peptide: HALC18-6_265
KeywordsDe novo protein design / Computational protein design / Machine learning / Hallucination / homo-oligomers / DE NOVO PROTEIN
Biological speciesEscherichia coli (E. coli) / Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsWicky BIM / Milles LF / Courbet AC / Baker D
Funding support United States, 3 items
OrganizationGrant numberCountry
Other private United States
Other governmentS10OD032290 United States
Other governmentP30 CA015704-40 United States
Citation
Journal: Science / Year: 2022
Title: Hallucinating symmetric protein assemblies.
Authors: B I M Wicky / L F Milles / A Courbet / R J Ragotte / J Dauparas / E Kinfu / S Tipps / R D Kibler / M Baek / F DiMaio / X Li / L Carter / A Kang / H Nguyen / A K Bera / D Baker /
Abstract: Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination ...Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.
#1: Journal: BioRxiv / Year: 2022
Title: Hallucinating protein assemblies
Authors: Wicky BIM / Milles LF / Courbet A / Baker D
History
DepositionJul 19, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27659.png

Downloads & links

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Map

FileDownload / File: emd_27659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-1.4184564 - 1.8299394
Average (Standard dev.)-0.000034245608 (±0.021343922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 371.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27659_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

Fileemd_27659_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_27659_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : De novo hallucinated homooligomer of C18-C6 symmetry, design HALC...

EntireName: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265.
Components
  • Complex: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265.
    • Protein or peptide: HALC18-6_265

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Supramolecule #1: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC...

SupramoleculeName: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: HALC18-6_265

MacromoleculeName: HALC18-6_265 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: NIKIPNPKDL SELLKKLGEG LKGLPNLKTL TLTLSNIELP EDADLSPGAE GLGEGLKGLP NLETLTFTIS NIKIPNPKD LSELLKKLGE GLKGLPNLKT LTLTLSNIEL PEDADLSPGA EGLGEGLKGL PNLETLTFTI S NIKIPNPK DLSELLKKLG EGLKGLPNLK ...String:
NIKIPNPKDL SELLKKLGEG LKGLPNLKTL TLTLSNIELP EDADLSPGAE GLGEGLKGLP NLETLTFTIS NIKIPNPKD LSELLKKLGE GLKGLPNLKT LTLTLSNIEL PEDADLSPGA EGLGEGLKGL PNLETLTFTI S NIKIPNPK DLSELLKKLG EGLKGLPNLK TLTLTLSNIE LPEDADLSPG AEGLGEGLKG LPNLETLTFT IS

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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 chlorideSodium 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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33607
FSC plot (resolution estimation)

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