8YNU | pdb_00008ynu

Crystal structure of the myb domain of S.pombe Tbf1 in the P222 space group

• PDB DOI: https://doi.org/10.2210/pdb8YNU/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-12 Released: 2025-04-09 
• Deposition Author(s): Zhou, Y.Z., Wu, Z.F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.232 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structural and functional insights into yeast Tbf1 as an atypical telomeric repeat-binding factor.

Wu, Z., Gu, X., Zha, L., Yang, Q., Zhou, Y., Zeng, Z.

(2024) Structure 32: 889-898.e3

• PubMed: 38677290 
• DOI: https://doi.org/10.1016/j.str.2024.04.002
• Primary Citation Related Structures: 
  8YNU


• PubMed Abstract: 
  

  Telomeric repeat-binding factor 1 (Tbf1) has a similar architecture as the TRF family of telomeric proteins and plays important roles in both telomere homeostasis and ribosome regulation. However, the molecular basis of why Tbf1 has such different functions compared to other TRFs remains unclear. Here, we present the crystal structures of the TRF homology (TRFH) and Myb-L domains from Schizosaccharomyces pombe Tbf1 (spTbf1). TRFH-mediated homodimerization is essential for spTbf1 stability. Importantly, spTbf1 _TRFH lacks the conserved docking motif for interactions with telomeric proteins, explaining why spTbf1 does not participate in the assembly of the shelterin complex. Finally, structural and biochemical analyses demonstrate that TRFH and Myb-L domains as well as the loop region of spTbf1 coordinate to recognize S. pombe telomeric double-stranded DNA. Overall, our findings provide structural and functional insights into how fungi Tbf1 acts as an atypical telomeric repeat-binding factor, which helps to understand the evolution of TRFH-containing telomeric proteins.

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Organizational Affiliation: 
• Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China. Electronic address: [e-mail].
State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China. Electronic address: [e-mail].
Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.21 kDa 
• Atom Count: 1,403 
• Modeled Residue Count: 158 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Telomeric DNA-binding factor trf1	A, B	80	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: trf1, SPBC19G7.13
UniProt
Find proteins for Q6E434 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q6E434  Go to UniProtKB:  Q6E434

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.232 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.393	α = 90
b = 62.23	β = 90
c = 86.773	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Zhou, Y.Z., Wu, Z.F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release