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- PDB-8ui2: T33-ml28 - Designed Tetrahedral Protein Cage Using Machine Learni... -

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Basic information

Entry
Database: PDB / ID: 8ui2
TitleT33-ml28 - Designed Tetrahedral Protein Cage Using Machine Learning Algorithms
Components
  • T33-ml28-redesigned-CutA-fold
  • T33-ml28-redesigned-tandem-BMC-T-fold
KeywordsDE NOVO PROTEIN / Nanohedra / protein cage / tetrahedral / de novo protein interface / machine learning / two components / ProteinMPNN / nanoparticle
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsCastells-Graells, R. / Meador, K. / Sawaya, M.R. / Yeates, T.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129854 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: Structure / Year: 2024
Title: A suite of designed protein cages using machine learning and protein fragment-based protocols.
Authors: Kyle Meador / Roger Castells-Graells / Roman Aguirre / Michael R Sawaya / Mark A Arbing / Trent Sherman / Chethaka Senarathne / Todd O Yeates /
Abstract: Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational ...Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational approaches to design a suite of tetrahedrally symmetric, self-assembling protein cages. For the generation of docked conformations, we emphasize a protein fragment-based approach, while for sequence design of the de novo interface, a comparison of knowledge-based and machine learning protocols highlights the power and increased experimental success achieved using ProteinMPNN. An analysis of design outcomes provides insights for improving interface design protocols, including prioritizing fragment-based motifs, balancing interface hydrophobicity and polarity, and identifying preferred polar contact patterns. In all, we report five structures for seven protein cages, along with two structures of intermediate assemblies, with the highest resolution reaching 2.0 Å using cryo-EM. This set of designed cages adds substantially to the body of available protein nanoparticles, and to methodologies for their creation.
History
DepositionOct 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold


Theoretical massNumber of molelcules
Total (without water)33,6862
Polymers33,6862
Non-polymers00
Water00
1
A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold

A: T33-ml28-redesigned-tandem-BMC-T-fold
B: T33-ml28-redesigned-CutA-fold


Theoretical massNumber of molelcules
Total (without water)404,23324
Polymers404,23324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11

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Components

#1: Protein T33-ml28-redesigned-tandem-BMC-T-fold


Mass: 21832.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pSAM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR
#2: Protein T33-ml28-redesigned-CutA-fold


Mass: 11853.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pSAM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR

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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: T33-ml28 Designed Tetrahedral Protein Cage Using Machine Learning
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: YES
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: LOBSTR
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 857483 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00427036
ELECTRON MICROSCOPYf_angle_d0.50436792
ELECTRON MICROSCOPYf_dihedral_angle_d4.1223840
ELECTRON MICROSCOPYf_chiral_restr0.0444404
ELECTRON MICROSCOPYf_plane_restr0.0054788

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