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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.263 (Depositor), 0.261 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8W8G

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.gendis.2024.101319
Primary Citation Related Structures:
8W8G

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54274
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	I [auth A], J [auth B], K [auth C], L [auth D]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.263 (Depositor), 0.261 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.