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- PDB-6xss: CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900 -

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Entry
Database: PDB / ID: 6xss
TitleCryoEM structure of designed helical fusion protein C4_nat_HFuse-7900
ComponentsC4_nat_HFuse-7900
KeywordsDE NOVO PROTEIN / helical bundle / helical repeat
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRedler, R.L. / Edman, N.I. / Baker, D. / Ekiert, D. / Bhabha, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1629214 United States
CitationJournal: Nat Commun / Year: 2021
Title: Design of multi-scale protein complexes by hierarchical building block fusion.
Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una ...Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una Nattermann / Evelyn Tsai / Ayesha Saleem / Cameron M Chow / Damian Ekiert / Gira Bhabha / David Veesler / David Baker /
Abstract: A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two ...A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: C4_nat_HFuse-7900
B: C4_nat_HFuse-7900
C: C4_nat_HFuse-7900
D: C4_nat_HFuse-7900


Theoretical massNumber of molelcules
Total (without water)114,8264
Polymers114,8264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5360 Å2
ΔGint-48 kcal/mol
Surface area50580 Å2

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Components

#1: Protein
C4_nat_HFuse-7900


Mass: 28706.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Lemo21 (DE3)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Designed fusion of helical bundle and helical repeat proteins
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21 Lemo21 (DE3)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 57.05 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
12RELION3.13D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144329 / Symmetry type: POINT

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