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- EMDB-59317: T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-59317
TitleT33-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Map dataFocused map for the T33-Fus-1B asymmetric unit, sharpened
Sample
  • Complex: T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
    • Protein or peptide: T33-Fus-1B-subunit
Keywordsprotein cage / tetrahedral / protein design / nanohedra / nanoparticle / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_59317.png

Downloads & links

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Map

FileDownload / File: emd_59317.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map for the T33-Fus-1B asymmetric unit, sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 320 pix.
= 386.88 Å		1.21 Å/pix.
x 320 pix.
= 386.88 Å		1.21 Å/pix.
x 320 pix.
= 386.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.209 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.59621936 - 1.0260223
Average (Standard dev.)0.00008601792 (±0.011807746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 386.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focused map for the T33-Fus-1B asymmetric unit, unsharpened

Fileemd_59317_additional_1.map
AnnotationFocused map for the T33-Fus-1B asymmetric unit, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus map for the T33-Fus-1B protein cage, sharpened

Fileemd_59317_additional_2.map
AnnotationConsensus map for the T33-Fus-1B protein cage, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus map for the T33-Fus-1B protein cage, sharpened

Fileemd_59317_additional_3.map
AnnotationConsensus map for the T33-Fus-1B protein cage, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B for the T33-Fus-1B asymmetric unit

Fileemd_59317_half_map_1.map
AnnotationHalf map B for the T33-Fus-1B asymmetric unit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A for the T33-Fus-1B asymmetric unit

Fileemd_59317_half_map_2.map
AnnotationHalf map A for the T33-Fus-1B asymmetric unit
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-Fus-1B asymmetric unit - Designed tetrahedral protein cage ba...

EntireName: T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Components
  • Complex: T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
    • Protein or peptide: T33-Fus-1B-subunit

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Supramolecule #1: T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage ba...

SupramoleculeName: T33-Fus-1B 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 design protein
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 630 KDa

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

MacromoleculeName: T33-Fus-1B-subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.809699 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDPQDLYTWE PKGLAVVDMA LAQESAGLVM LYHFDGYIDA GETGDQIVDQ VLDSLPHQVV ARFDHDRLVD YRARRPLLTF KRDTWSDYE EPTIEVRLVQ DATGAPFLFL SGPEPDVEWE RFAAAVGQIV ERLGVRLSVS FHGIPMGVPH TRPVGITPHG S RTDLVPGH ...String:
MDPQDLYTWE PKGLAVVDMA LAQESAGLVM LYHFDGYIDA GETGDQIVDQ VLDSLPHQVV ARFDHDRLVD YRARRPLLTF KRDTWSDYE EPTIEVRLVQ DATGAPFLFL SGPEPDVEWE RFAAAVGQIV ERLGVRLSVS FHGIPMGVPH TRPVGITPHG S RTDLVPGH RSPFEEAQVP GSAEALVEYR LAQAGHDVLG VAAHVPHYVA RSAYPDAALT VLEAITAATG LVLPGIAHSL RT DAHRTQT EIDRQIQEGD EELIALVRGL EARYDGAVID AQLKALKVIP VIAIDNAEDI IPLGKVLAEN GLPAAEITFR SDA AVEAIR LLRQAQPEML IGAGTILNGE QALAAKEAGA TFVVSPGFNP NTVRACREIG IPIVPGVNNP STVEAALEMG LTTL KFFPA EASGGISMVK SLVGPYGDIR LMPTGGITPS NIDNYLAIPQ VLACGGTWMV DKKLVTNGEW DEIARLTREI VEQVN PGHH HHHH

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 45s 0.1 bar 15 mA
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v5.0.4) / Details: The particles were expanded in T symmetry / Number images used: 2200000
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-33av:
T33-Fus-1B asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning

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