8H8N | pdb_00008h8n

Crystal structure of apo-R52Y/E56Y/R59Y/E63Y-rHLFr

• PDB DOI: https://doi.org/10.2210/pdb8H8N/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Equus caballus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-10-23 Released: 2023-10-04 
• Deposition Author(s): Hishikawa, Y., Noya, H., Maity, B., Abe, S., Ueno, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters by Using Protein Cages.

Hishikawa, Y., Noya, H., Nagatoishi, S., Yoshidome, T., Maity, B., Tsumoto, K., Abe, S., Ueno, T.

(2023) Chemistry 29: e202300488-e202300488

• PubMed: 37070368 
• DOI: https://doi.org/10.1002/chem.202300488
• Primary Citation Related Structures: 
  8H8L, 8H8M, 8H8N, 8H8O


• PubMed Abstract: 
  

  Multiple aromatic residues assemble to form higher ordered structures known as "aromatic clusters" in proteins and play essential roles in biological systems. However, the stabilization mechanism and dynamic behavior of aromatic clusters remain unclear. This study describes designed aromatic interactions confined within a protein cage to reveal how aromatic clusters affect protein stability. The crystal structures and calorimetric measurements indicate that the formation of inter-subunit phenylalanine clusters enhance the interhelix interactions and increase the melting temperature. Theoretical calculations suggest that this is caused by the transformation of the T-shaped geometry into π-π stacking at high temperatures, and the hydration entropic gain. Thus, the isolated nanoenvironment in a protein cage allows reconstruction and detailed analysis of multiple clustering residues for elucidating the mechanisms of various biomolecular interactions in nature which can be applied to design of bionanomaterials.

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Organizational Affiliation: 
• School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259-B55, Midori-ku, 226-8501, Yokohama, Japan.
The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, 108-8639, Minato-ku, Tokyo, Japan.
Department of Applied Physics, Graduate School of Engineering, Tohoku University, Aoba 6-6-05, Aramaki, Aoba-ku, 980-8579, Sendai, Japan.
Department of Bioengineering, School of Engineering, The University of Tokyo Hongo 7-3-1, 113-8656, Bunkyo-ku, Tokyo, Japan.
Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, 226-8501, Yokohama, Japan.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 21.11 kDa 
• Atom Count: 1,775 
• Modeled Residue Count: 174 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A	174	Equus caballus	Mutation(s): 4  Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.877	α = 90
b = 181.877	β = 90
c = 181.877	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Hishikawa, Y., Noya, H., Maity, B., Abe, S., Ueno, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary