4ZK7 | pdb_00004zk7

Crystal structure of rescued two-component self-assembling tetrahedral cage T33-31

• PDB DOI: https://doi.org/10.2210/pdb4ZK7/pdb

• Classification: PROTEIN BINDING
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-30 Released: 2015-07-29 
• Deposition Author(s): Liu, Y., Cascio, D., Sawaya, M.R., Bale, J., Collazo, M.J., Park, R., King, N., Baker, D., Yeates, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.239 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.

Bale, J.B., Park, R.U., Liu, Y., Gonen, S., Gonen, T., Cascio, D., King, N.P., Yeates, T.O., Baker, D.

(2015) Protein Sci 24: 1695-1701

• PubMed: 26174163 
• DOI: https://doi.org/10.1002/pro.2748
• Primary Citation Related Structures: 
  4ZK7


• PubMed Abstract: 
  

  We recently reported the development of a computational method for the design of coassembling multicomponent protein nanomaterials. While four such materials were validated at high-resolution by X-ray crystallography, low yield of soluble protein prevented X-ray structure determination of a fifth designed material, T33-09. Here we report the design and crystal structure of T33-31, a variant of T33-09 with improved soluble yield resulting from redesign efforts focused on mutating solvent-exposed side chains to charged amino acids. The structure is found to match the computational design model with atomic-level accuracy, providing further validation of the design approach and demonstrating a simple and potentially general means of improving the yield of designed protein nanomaterials.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, Washington, 98195.
Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, 98195.
Department of Chemistry and Biochemistry, UCLA, Los Angeles, California, 90095.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147.
Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California, 90095.
Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, scanning transmission electron microscopy

Macromolecule Content 

• Total Structure Weight: 324.48 kDa 
• Atom Count: 20,678 
• Modeled Residue Count: 2,646 
• Deposited Residue Count: 2,892 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate mutase	A, B, C, D, E, F, G, H, I, J, K, L	130	Thermus thermophilus HB8	Mutation(s): 6  Gene Names: TTHA0868 EC: 5.4.99.5
UniProt
Find proteins for Q5SJY4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJY4  Go to UniProtKB:  Q5SJY4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Divalent-cation tolerance protein CutA	M, N, O, P, Q, R, S, T, U, V, W, X	111	Thermus thermophilus HB8	Mutation(s): 13  Gene Names: cutA, TTHA1356
UniProt
Find proteins for Q7SIA8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q7SIA8  Go to UniProtKB:  Q7SIA8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.239 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.1	α = 90
b = 128.4	β = 90
c = 204.7	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Liu, Y., Cascio, D., Sawaya, M.R., Bale, J., Collazo, M.J., Park, R., King, N., Baker, D., Yeates, T.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references