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- EMDB-47128: Cryo-EM structure of the T33-549 tetrahedral cage -

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Basic information

Entry
Database: EMDB / ID: EMD-47128
TitleCryo-EM structure of the T33-549 tetrahedral cage
Map datacryo-EM map with T symmetry applied
Sample
  • Complex: T33-549 tetrahedral cage
    • Protein or peptide: T33-549_B
    • Protein or peptide: T33-549_A
Keywordsnanomaterial / protein cages / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsRedler R / Coudray N / Lubner J / Wang S / Baker D / Ekiert DC / Bhabha G
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128777 United States
CitationJournal: bioRxiv / Year: 2024
Title: Bond-centric modular design of protein assemblies.
Authors: Shunzhi Wang / Andrew Favor / Ryan Kibler / Joshua Lubner / Andrew J Borst / Nicolas Coudray / Rachel L Redler / Huat Thart Chiang / William Sheffler / Yang Hsia / Zhe Li / Damian C Ekiert / ...Authors: Shunzhi Wang / Andrew Favor / Ryan Kibler / Joshua Lubner / Andrew J Borst / Nicolas Coudray / Rachel L Redler / Huat Thart Chiang / William Sheffler / Yang Hsia / Zhe Li / Damian C Ekiert / Gira Bhabha / Lilo D Pozzo / David Baker /
Abstract: We describe a modular bond-centric approach to protein nanomaterial design inspired by the rich diversity of chemical structures that can be generated from the small number of atomic valencies and ...We describe a modular bond-centric approach to protein nanomaterial design inspired by the rich diversity of chemical structures that can be generated from the small number of atomic valencies and bonding interactions. We design protein building blocks with regular coordination geometries and bonding interactions that enable the assembly of a wide variety of closed and opened nanomaterials using simple geometrical principles. Experimental characterization confirms successful formation of more than twenty multi-component polyhedral protein cages, 2D arrays, and 3D protein lattices, with a high (10-50 %) success rate and electron microscopy data closely matching the corresponding design models. Because of the modularity, individual building blocks can assemble with different partners to generate distinct regular assemblies, resulting in an economy of parts and enabling the construction of reconfigurable systems.
History
DepositionSep 25, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47128.png

Downloads & links

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Map

FileDownload / File: emd_47128.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map with T symmetry applied
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 494.4 Å		1.24 Å/pix.
x 400 pix.
= 494.4 Å		1.24 Å/pix.
x 400 pix.
= 494.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.236 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.12652554 - 0.28671864
Average (Standard dev.)-0.00016829121 (±0.009639557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 494.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47128_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_47128_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47128_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : T33-549 tetrahedral cage

EntireName: T33-549 tetrahedral cage
Components
  • Complex: T33-549 tetrahedral cage
    • Protein or peptide: T33-549_B
    • Protein or peptide: T33-549_A

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Supramolecule #1: T33-549 tetrahedral cage

SupramoleculeName: T33-549 tetrahedral cage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: T33-549_B

MacromoleculeName: T33-549_B / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.48143 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGGKELEIVA RLQQLNIELA RKLLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEQ EIRKAEAESL RLTAEAAAD AARKAALRMG DERVRRLAAE LVRLAQEAAE EATRDPNSSD QNEALRLIIL AILAAVKALD AAIRTGDPEV R ELARELVR ...String:
MGGKELEIVA RLQQLNIELA RKLLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEQ EIRKAEAESL RLTAEAAAD AARKAALRMG DERVRRLAAE LVRLAQEAAE EATRDPNSSD QNEALRLIIL AILAAVKALD AAIRTGDPEV R ELARELVR LAVEAAEEVQ RNPSSSDVNE ALKLIVEAIE AAVQALEAAI EAGDPREREK ARELVRLAVE AAEEVQRNPS SK EVNVKLK AIVVAIKVFV LKLSGTSEDE IAEEIARDIS ELIRKLKEDG SSYEDICEAV ATVVDMVVEA LKRAGTSEDE IAE IVARVI SEVIRTLKES GSSYEVICEC VARIVAAIVE ALKRSGTSEE EIAEIVARVI QEVIRTLKES GSSYEVIREC LRRI LEEVI EALKRSGVDS SEIVLIIIKI AVAVMGVTME EHRSGNEVKV VIKGLHESQQ EELLELVLRA AELAGVRVRI RFKGD TVTI VVRGGGWGGS ENLYFQSGGL EHHHHHH

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Macromolecule #2: T33-549_A

MacromoleculeName: T33-549_A / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 42.75202 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSEEKIEKL LEELTASTAE LKRATASLRA ITEELKKNPS EDALVEHNRA IVEHNAIIVE NNRIIATVLL AIVAAIATNE ATLAADKAK EAGASEVAKL AKKVLEEAEE LAKENDSEEA LKVVKAIADA AKAAAEAARE GKTEVAKLAL KVLEEAIELA K ENRSEEAL ...String:
MGSEEKIEKL LEELTASTAE LKRATASLRA ITEELKKNPS EDALVEHNRA IVEHNAIIVE NNRIIATVLL AIVAAIATNE ATLAADKAK EAGASEVAKL AKKVLEEAEE LAKENDSEEA LKVVKAIADA AKAAAEAARE GKTEVAKLAL KVLEEAIELA K ENRSEEAL DVVRAIALAA YAAARAAQAG ATDFAKDALR KLEEAIEEAK KRRSEKALRE VYTIALKAAV QAAEAAVRAQ PG SNRAKSA LEIILQAAEE LAKLPDPEAL KDAVKAAEKV VREQPGSNLA KKALEIILRA AAALANLPDP ESRKEADKAA DKV RREQPG SELAVVAAII SAVARMGVKM ELHPSGNEVK VVIKGLHIKQ QRQLYRDVRE AAKKAGVEVE IEVEGDTVTI VVRG

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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

Concentration8.5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mM(hydroxymethyl)aminomethane
300.0 mMsodium chlorideNaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 12276 / Average exposure time: 2.0 sec. / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 300 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: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4841024
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 6 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 662340
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 9 / Avg.num./class: 83500 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: design model
DetailsSecondary structure restraints due to lower resolution
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9drl:
Cryo-EM structure of the T33-549 tetrahedral cage

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