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- EMDB-59318: T33-Fus-2 asymmetric unit - Designed tetrahedral protein cage bas... -

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Basic information

Entry
Database: EMDB / ID: EMD-59318
TitleT33-Fus-2 asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Map dataT33-Fus2 protein cage asymmetric unit focused map sharpened
Sample
  • Complex: T33-Fus2 asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
    • Protein or peptide: T33-Fus-2-subunit
Keywordsprotein cage / tetrahedral / protein design / nanohedra / nanoparticle / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsSan Segundo-Acosta P / LeCoq J / Boskovic J / Aglietti RA / Bowers P / Yeates TO / Castells-Graells R
Funding support Spain, European Union, 3 items
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 RA / Bowers P / Yeates TO / Castells-Graells R
History
DepositionAug 4, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59318.png

Downloads & links

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Map

FileDownload / File: emd_59318.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT33-Fus2 protein cage asymmetric unit focused map sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 256 pix.
= 297.6 Å		1.16 Å/pix.
x 256 pix.
= 297.6 Å		1.16 Å/pix.
x 256 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.8439794 - 3.0069807
Average (Standard dev.)0.0017162835 (±0.033232477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: T33-Fus2 protein cage asymmetric unit focused map unsharpened

Fileemd_59318_additional_1.map
AnnotationT33-Fus2 protein cage asymmetric unit focused map unsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T33-Fus2 protein cage asymmetric unit focused half map A

Fileemd_59318_half_map_1.map
AnnotationT33-Fus2 protein cage asymmetric unit focused half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T33-Fus2 protein cage asymmetric unit focused half map B

Fileemd_59318_half_map_2.map
AnnotationT33-Fus2 protein cage asymmetric unit focused half 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 : T33-Fus2 asymmetric unit - Designed tetrahedral protein cage base...

EntireName: T33-Fus2 asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Components
  • Complex: T33-Fus2 asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
    • Protein or peptide: T33-Fus-2-subunit

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Supramolecule #1: T33-Fus2 asymmetric unit - Designed tetrahedral protein cage base...

SupramoleculeName: T33-Fus2 asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: De novo protein design
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 640 KDa

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Macromolecule #1: T33-Fus-2-subunit

MacromoleculeName: T33-Fus-2-subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 53.243219 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MREYEPGQPG MYELEFPAPQ LSSSDGRGPV LVHALEGFSD AGHAIRLAAA HLKAALDTEL VASFAIDELL DYRSRRPLMT FKTDHFTHS DDPELSLYAL RDSIGTPFLL LAGLEPDLKW ERFITAVRLL AERLGVRQTI GLGTVPMAVP HTRPITMTAH S NNRELISD ...String:
MREYEPGQPG MYELEFPAPQ LSSSDGRGPV LVHALEGFSD AGHAIRLAAA HLKAALDTEL VASFAIDELL DYRSRRPLMT FKTDHFTHS DDPELSLYAL RDSIGTPFLL LAGLEPDLKW ERFITAVRLL AERLGVRQTI GLGTVPMAVP HTRPITMTAH S NNRELISD FTPSISEIQV PGSASNLLEY RMAQHGHEVV GFTVHVPHYL TQTDYPAAAQ ALLEQVAKTG SLQLPLAVLA EA AAEVQAK IDEQVQASAE VAQVVAALER QYAAAQAKSA VARRLGKVTA SRVADVMTKT KSGYAASRQN YMAELIAQRL TGT QEIRFS NAAMQRGTEL EPHARARYII ETGEIVTEVG LIDHPTIAGF GASPDGLVGD TGLIEIKCPN TWTHIETIKT GKPK PEYIK QMQTQMACTG RQWCDFVSYD DRLPDDMQYF RTRIERDDAL IAEIETEVSA FLAELEAEIE YLKRKAAKLA GHHHH HH

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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

Concentration0.3 mg/mL
BufferpH: 8 / Details: 30 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blotting 3 seconds, blot force 0.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v5.0.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial model generated de novo by ab-initio reconstruction in CryoSPARC from the experimental particle set
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v5.0.4) / Details: Particles were T-symmetry expanded / Number images used: 560640
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v5.0.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v5.0.4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v5.0.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: The initial model consisted of a de novo design protein
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-33aw:
T33-Fus-2 asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning

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