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- PDB-33av: T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage ba... -

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Basic information

Entry
Database: PDB / ID: 33av
TitleT33-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
ComponentsT33-Fus-1B-subunit
KeywordsDE NOVO PROTEIN / protein cage / tetrahedral / protein design / nanohedra / nanoparticle
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSan Segundo-Acosta, P. / LeCoq, J. / Boskovic, J. / Aglietti, R.A. / Bowers, P. / Yeates, T.O. / Castells-Graells, R.
Funding support Spain, European Union, 3items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2024-161096NA-I00 Spain
European Union (EU)C005/24-ED CV1European Union
Generalitat de CatalunyaIU16-014045 Spain
CitationJournal: To Be Published
Title: Design and structure of protein cages based on helical fusion and machine learning
Authors: San Segundo-Acosta, P. / LeCoq, J. / Boskovic, J. / Aglietti, R.A. / Bowers, P. / Yeates, T.O. / Castells-Graells, R.
History
DepositionAug 4, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T33-Fus-1B-subunit


Theoretical massNumber of molelcules
Total (without water)52,8101
Polymers52,8101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein T33-Fus-1B-subunit


Mass: 52809.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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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-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Type: COMPLEX / Details: De novo design protein / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.63 MDa / Experimental value: YES
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 30 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 45s 0.1 bar 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blotting 3 seconds, blot force 0

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv5.0.4particle selection
2EPUimage acquisition
4cryoSPARCv5.0.4CTF correction
7UCSF ChimeraX1.11.1model fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARCv5.0.4initial Euler assignment
11cryoSPARCv5.0.4final Euler assignment
12cryoSPARCv5.0.4classification
13cryoSPARCv5.0.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2200000 / Algorithm: FOURIER SPACE / Details: The particles were expanded in T symmetry / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: The initial model consisted of a de novo design protein
Source name: Other / Type: in silico model
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311060
ELECTRON MICROSCOPYf_angle_d0.63115094
ELECTRON MICROSCOPYf_dihedral_angle_d5.2831560
ELECTRON MICROSCOPYf_chiral_restr0.0461754
ELECTRON MICROSCOPYf_plane_restr0.0051999

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