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

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Basic information

Entry
Database: PDB / ID: 9drl
TitleCryo-EM structure of the T33-549 tetrahedral cage
Components
  • T33-549_A
  • T33-549_B
KeywordsDE NOVO PROTEIN / nanomaterial / protein cages
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsRedler, R. / Coudray, N. / Lubner, J. / Wang, S. / Baker, D. / Ekiert, D.C. / Bhabha, G.
Funding support United States, 3items
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
Citation
Journal: Nat Mater / Year: 2025
Title: Bond-centric modular design of protein assemblies.
Authors: Shunzhi Wang / Andrew Favor / Ryan D Kibler / Joshua M Lubner / Andrew J Borst / Nicolas Coudray / Rachel L Redler / Huat Thart Chiang / William Sheffler / Yang Hsia / Neville P Bethel / Zhe ...Authors: Shunzhi Wang / Andrew Favor / Ryan D Kibler / Joshua M Lubner / Andrew J Borst / Nicolas Coudray / Rachel L Redler / Huat Thart Chiang / William Sheffler / Yang Hsia / Neville P Bethel / Zhe Li / Damian C Ekiert / Gira Bhabha / Lilo D Pozzo / David Baker /
Abstract: Directional interactions that generate regular coordination geometries are a powerful means of guiding molecular and colloidal self-assembly, but implementing such high-level interactions with ...Directional interactions that generate regular coordination geometries are a powerful means of guiding molecular and colloidal self-assembly, but implementing such high-level interactions with proteins remains challenging due to their complex shapes and intricate interface properties. Here we describe a modular approach to protein nanomaterial design inspired by the rich chemical diversity that can be generated from the small number of atomic valencies. We design protein building blocks using deep learning-based generative tools, incorporating regular coordination geometries and tailorable bonding interactions that enable the assembly of diverse closed and open architectures guided by simple geometric principles. Experimental characterization confirms the successful formation of more than 20 multicomponent polyhedral protein cages, two-dimensional arrays and three-dimensional protein lattices, with a high (10%-50%) success rate and electron microscopy data closely matching the corresponding design models. Due to 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 networks for designer nanomaterials.
#1: Journal: 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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.2Oct 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T33-549_B
B: T33-549_A
C: T33-549_B
D: T33-549_A
E: T33-549_B
F: T33-549_A
G: T33-549_B
H: T33-549_A
I: T33-549_B
J: T33-549_A
K: T33-549_B
L: T33-549_A
M: T33-549_B
N: T33-549_A
O: T33-549_B
P: T33-549_A
Q: T33-549_B
R: T33-549_A
S: T33-549_B
T: T33-549_A
U: T33-549_B
V: T33-549_A
W: T33-549_B
X: T33-549_A


Theoretical massNumber of molelcules
Total (without water)1,190,80124
Polymers1,190,80124
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
T33-549_B


Mass: 56481.430 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
T33-549_A


Mass: 42752.020 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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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: T33-549 tetrahedral cage / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM(hydroxymethyl)aminomethane1
2300 mMsodium chlorideNaCl1
SpecimenConc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 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 magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 58.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12276
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.18.2_3874:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4841024
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 662340 / Algorithm: BACK PROJECTION / Num. of class averages: 6 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Secondary structure restraints due to lower resolution
Atomic model buildingDetails: design model / Source name: Other / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00681252
ELECTRON MICROSCOPYf_angle_d0.751109440
ELECTRON MICROSCOPYf_dihedral_angle_d4.37611520
ELECTRON MICROSCOPYf_chiral_restr0.05113488
ELECTRON MICROSCOPYf_plane_restr0.00414304

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