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- EMDB-27658: cryoEM map of de novo hallucinated homooligomer of C15-C5 symmetr... -

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Basic information

Entry
Database: EMDB / ID: EMD-27658
TitlecryoEM map of de novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
Map dataEM map of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Sample
  • Complex: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
    • Protein or peptide: HALC15-5_262
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: 3.69 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) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27658.png

Downloads & links

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Map

FileDownload / File: emd_27658.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.3681349 - 1.9633029
Average (Standard dev.)0.0000817919 (±0.0126535995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27658_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 C15/C5 symmetric hallucinated protein...

Fileemd_27658_half_map_1.map
Annotationhalf map A of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of C15/C5 symmetric hallucinated protein...

Fileemd_27658_half_map_2.map
Annotationhalf map B of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
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 C15-C5 symmetry, design HALC...

EntireName: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
Components
  • Complex: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
    • Protein or peptide: HALC15-5_262

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Supramolecule #1: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC...

SupramoleculeName: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: HALC15-5_262

MacromoleculeName: HALC15-5_262 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant expressionOrganism: Expression vector pET-mod (others)
SequenceString: DVPLTDPKNL NEFLYALGEG LKGMKNLKKL TLTFPSNPLT IPGDISEGFR ELGEGLKGMK NLEELTVTFN DVPLTDPKN LNEFLYALGE GLKGMKNLKK LTLTFPSNPL TIPGDISEGF RELGEGLKGM KNLEELTVTF N DVPLTDPK NLNEFLYALG EGLKGMKNLK ...String:
DVPLTDPKNL NEFLYALGEG LKGMKNLKKL TLTFPSNPLT IPGDISEGFR ELGEGLKGMK NLEELTVTFN DVPLTDPKN LNEFLYALGE GLKGMKNLKK LTLTFPSNPL TIPGDISEGF RELGEGLKGM KNLEELTVTF N DVPLTDPK NLNEFLYALG EGLKGMKNLK KLTLTFPSNP LTIPGDISEG FRELGEGLKG MKNLEELTVT FN

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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
GridModel: C-flat-2/2
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 K2 SUMMIT (4k x 4k) / 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 reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 563158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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