8UF0

T33-ml23 - Designed Tetrahedral Protein Cage Using Machine Learning Algorithms

• PDB DOI:  https://doi.org/10.2210/pdb8UF0/pdb
• EM Map EMD-42181: EMDB EMDataResource

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-03 Released: 2023-11-15 
• Deposition Author(s): Castells-Graells, R., Meador, K., Sawaya, M.R., Yeates, T.O.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A suite of designed protein cages using machine learning algorithms and protein fragment-based protocols

Meador, K., Castells-Graells, R., Aguirre, R., Sawaya, M.R., Arbing, M.A., Sherman, T., Senarathne, C., Yeates, T.O.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 33.23 kDa 
• Atom Count: 2,250 
• Modelled Residue Count: 288 
• Deposited Residue Count: 306 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T33-ml23-redesigned-CutA-fold	A	101	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T33-ml23-redesigned-tandem-BMC-T-fold	B	205	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Castells-Graells, R., Meador, K., Sawaya, M.R., Yeates, T.O.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM129854
Department of Energy (DOE, United States)	United States	DE-FC02-02ER63421

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release