8W8G | pdb_00008w8g

Crystal structure of human TRF1 with PinX1

• PDB DOI: https://doi.org/10.2210/pdb8W8G/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-02 Released: 2024-09-04 
• Deposition Author(s): Lei, M., Wu, J.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.263 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

PinX1 suppresses cancer progression by inhibiting telomerase activity in cervical squamous cell carcinoma and endocervical adenocarcinoma.

Weng, Y., Yan, X., Chen, B., Bian, Z., Ge, Y., Lu, H., He, S., Wu, J., Chen, Y., Lei, M., Zhang, Y.

(2025) Genes Dis 12: 101319-101319

• PubMed: 39634130 
• DOI: https://doi.org/10.1016/j.gendis.2024.101319
• Primary Citation of Related Structures:  
  8W8G

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Organizational Affiliation: 

Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.38 kDa 
• Atom Count: 7,064 
• Modelled Residue Count: 868 
• Deposited Residue Count: 928 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Telomeric repeat-binding factor 1	A, B, C, D	212	Homo sapiens	Mutation(s): 0  Gene Names: TERF1
UniProt & NIH Common Fund Data Resources
Find proteins for P54274 (Homo sapiens) Explore P54274  Go to UniProtKB:  P54274
PHAROS:  P54274 GTEx:  ENSG00000147601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PIN2/TERF1-interacting telomerase inhibitor 1	E, F, G, H	20	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	I [auth A], J [auth B], K [auth C], L [auth D]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.263 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.396	α = 90
b = 89.195	β = 90
c = 113.716	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Lei, M., Wu, J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references, Structure summary