8YOZ | pdb_00008yoz

Crystal structure of the small zinc-finger protein ZifS (TTHA0897) from Thermus thermophilus HB8.

• PDB DOI: https://doi.org/10.2210/pdb8YOZ/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-14 Released: 2025-03-19 
• Deposition Author(s): Kurinami, S., Fukui, K., Murakawa, T., Baba, S., Kumasaka, T., Okanishi, H., Kanai, Y., Yano, T., Masui, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

The crystal structure of the small zinc-finger protein ZifS from Thermus thermophilus HB8.

Kurinami, S., Fukui, K., Murakawa, T., Baba, S., Kumasaka, T., Okanishi, H., Kanai, Y., Yano, T., Masui, R.

(2025) J Biochem 178: 121-133

• PubMed: 40441711 
• DOI: https://doi.org/10.1093/jb/mvaf028
• Primary Citation Related Structures: 
  8YOZ


• PubMed Abstract: 
  

  Zinc finger domains are important interaction modules for binding to nucleic acids, proteins, lipids, and small molecules. Many small-sized zinc finger proteins are encoded in bacterial genomes, but most of them have not been functionally annotated. We focused on TTHA0897, ZifS, as a small zinc finger protein from the extremely thermophilic eubacterium Thermus thermophilus HB8. In vivo experiments suggested that the cellular function of ZifS is related to the growth transition of T. thermophilus from the lag to the exponential phase under nutritionally limited conditions. In vitro biochemical experiments, including electrophoretic mobility shift assay and pull-down assay, yielded no clues about molecular functions of ZifS. X-ray crystallographic analysis revealed that the dimeric ZifS globally forms a cylinder-like structure, although ZifS dimer has no overall structural similarity to other known zinc finger proteins. The zinc ion-binding manner of ZifS fitted the characteristics of the zinc ribbon fold, which are mostly found in domains from proteins involved in the transcriptional and translational machinery. The crystal structure of ZifS is the first experimental insight into the molecular structure of this protein family, revealing several conserved features that may be functionally relevant.

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Organizational Affiliation: 
• Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.
Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan.
The Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Hyogo 679-5198, Japan.
Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan.
Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Suita, Osaka 565-0871, Japan.
Department of Metabolic Reprogramming and Signal Regulation, Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka 565-0871, Japan.
Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.47 kDa 
• Atom Count: 1,254 
• Modeled Residue Count: 156 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor zinc-finger domain-containing protein	A, B	82	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0897
UniProt
Find proteins for Q5SJV5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJV5  Go to UniProtKB:  Q5SJV5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.12	α = 90
b = 67.01	β = 90
c = 81.92	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
XDS	data reduction
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Kurinami, S., Fukui, K., Murakawa, T., Baba, S., Kumasaka, T., Okanishi, H., Kanai, Y., Yano, T., Masui, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Database references
• Version 1.2: 2025-08-20
  Changes: Database references