8UDN | pdb_00008udn

A Stable Heterotrimeric Foldon with Minimum Mutation

• PDB DOI: https://doi.org/10.2210/pdb8UDN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Tequatrovirus T4
• Expression System: synthetic construct
• Mutation(s): No 


• Deposited: 2023-09-28 Released: 2025-05-14 
• Deposition Author(s): Bingman, C.A., Liu, X., Roberts, D.S., Gellman, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 
  0.158 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Rational Design of a Foldon-Derived Heterotrimer Guided by Quantitative Native Mass Spectrometry.

Liu, X., Roberts, D.S., Bingman, C.A., Ge, Y., Gellman, S.H.

(2025) J Am Chem Soc 147: 23819-23826

• PubMed: 40580137 
• DOI: https://doi.org/10.1021/jacs.5c06094
• Primary Citation of Related Structures:  
  8UDN


• PubMed Abstract: 
  

  Designing stable hetero-oligomeric protein complexes with defined intersubunit stoichiometry remains a significant challenge. In this study, we report the design of a highly selective heterotrimeric assembly derived from the well-known foldon homotrimer. We generated an aab heterotrimer by replacing glutamine 11 with glutamic acid, to destabilize the homotrimer, and replacing valine 14 with either alanine or leucine, to stabilize the hydrophobic core of the heterotrimer. Native mass spectrometry (MS) was essential for guiding the design process, enabling precise characterization of oligomeric states and their equilibrium distributions. The heterotrimer structure was validated by X-ray crystallography. Our findings highlight the effectiveness of combining rational design with native MS to develop specific hetero-oligomeric assemblies.

---

Organizational Affiliation: 
• Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Department of Cell and Regenerative Biology, University of Wisconsin - Madison, Madison, Wisconsin 53705, United States.
Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 9.39 kDa 
• Atom Count: 2,358 
• Modeled Residue Count: 84 
• Deposited Residue Count: 84 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibritin	A, B, C	27	Tequatrovirus T4	Mutation(s): 0  Gene Names: wac
UniProt
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free:  0.158 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38UDN

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.854	α = 90
b = 32.854	β = 90
c = 75.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Bingman, C.A., Liu, X., Roberts, D.S., Gellman, S.H.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R01GM056414-24

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Database references
• Version 1.2: 2025-07-16
  Changes: Database references
• Version 1.3: 2025-07-23
  Changes: Database references