5GU0 | pdb_00005gu0

Crystal structure of Au.CL-apo-E45C/R52C-rHLFr

• PDB DOI: https://doi.org/10.2210/pdb5GU0/pdb

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


• Deposited: 2016-08-24 Released: 2017-03-29 
• Deposition Author(s): Maity, B., Abe, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Observation of gold sub-nanocluster nucleation within a crystalline protein cage

Maity, B., Abe, S., Ueno, T.

(2017) Nat Commun 8: 14820-14820

• PubMed: 28300064 
• DOI: https://doi.org/10.1038/ncomms14820
• Primary Citation Related Structures: 
  5GU0, 5GU1, 5GU2, 5GU3


• PubMed Abstract: 
  

  Protein scaffolds provide unique metal coordination environments that promote biomineralization processes. It is expected that protein scaffolds can be developed to prepare inorganic nanomaterials with important biomedical and material applications. Despite many promising applications, it remains challenging to elucidate the detailed mechanisms of formation of metal nanoparticles in protein environments. In the present work, we describe a crystalline protein cage constructed by crosslinking treatment of a single crystal of apo-ferritin for structural characterization of the formation of sub-nanocluster with reduction reaction. The crystal structure analysis shows the gradual movement of the Au ions towards the centre of the three-fold symmetric channels of the protein cage to form a sub-nanocluster with accompanying significant conformational changes of the amino-acid residues bound to Au ions during the process. These results contribute to our understanding of metal core formation as well as interactions of the metal core with the protein environment.

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Organizational Affiliation: 
• School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, 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)

Macromolecule Content 

• Total Structure Weight: 22.02 kDa 
• Atom Count: 1,458 
• Modeled Residue Count: 170 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A [auth X]	174	Equus caballus	Mutation(s): 2  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
AU	B [auth X], C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
CD	J [auth X], K [auth X], L [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	M [auth X], N [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	O [auth X], P [auth X]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.892	α = 90
b = 180.892	β = 90
c = 180.892	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Maity, B., Abe, S., Ueno, T.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations