8XV8 | pdb_00008xv8

Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.207 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8XV8

This is version 1.1 of the entry. See complete history

Literature

Defining ortholog-specific UHRF1 inhibition by STELLA for cancer therapy.

Bai, W.Xu, J.Gu, W.Wang, D.Cui, Y.Rong, W.Du, X.Li, X.Xia, C.Gan, Q.He, G.Guo, H.Deng, J.Wu, Y.Yen, R.C.Yegnasubramanian, S.Rothbart, S.B.Luo, C.Wu, L.Liu, J.Baylin, S.B.Kong, X.

(2025) Nat Commun 16: 474-474

  • DOI: https://doi.org/10.1038/s41467-024-55481-7
  • Primary Citation Related Structures: 
    8XV4, 8XV6, 8XV7, 8XV8

  • PubMed Abstract: 

    UHRF1 maintains DNA methylation by recruiting DNA methyltransferases to chromatin. In mouse, these dynamics are potently antagonized by a natural UHRF1 inhibitory protein STELLA, while the comparable effects of its human ortholog are insufficiently characterized, especially in cancer cells. Herein, we demonstrate that human STELLA (hSTELLA) is inadequate, while mouse STELLA (mSTELLA) is fully proficient in inhibiting the abnormal DNA methylation and oncogenic functions of UHRF1 in human cancer cells. Structural studies reveal a region of low sequence homology between these STELLA orthologs that allows mSTELLA but not hSTELLA to bind tightly and cooperatively to the essential histone-binding, linked tandem Tudor domain and plant homeodomain (TTD-PHD) of UHRF1, thus mediating ortholog-specific UHRF1 inhibition. For translating these findings to cancer therapy, we use a lipid nanoparticle (LNP)-mediated mRNA delivery approach in which the short mSTELLA, but not hSTELLA regions are required to reverse cancer-specific DNA hypermethylation and impair colorectal cancer tumorigenicity.


  • Organizational Affiliation
    • Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.

Macromolecule Content 

  • Total Structure Weight: 56.98 kDa 
  • Atom Count: 3,067 
  • Modeled Residue Count: 379 
  • Deposited Residue Count: 488 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1
A, C, E, G
75Homo sapiensMutation(s): 0 
Gene Names: UHRF1ICBP90NP95RNF106
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens)
Explore Q96T88 
Go to UniProtKB:  Q96T88
PHAROS:  Q96T88
GTEx:  ENSG00000276043 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96T88
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Developmental pluripotency-associated protein 3
B, D, F, H
47Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6W0C5 (Homo sapiens)
Explore Q6W0C5 
Go to UniProtKB:  Q6W0C5
PHAROS:  Q6W0C5
GTEx:  ENSG00000187569 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6W0C5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth C]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth E],
R [auth E],
S [auth E],
T [auth G],
U [auth G],
V [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.207 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.029α = 90
b = 46.02β = 112.76
c = 82.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references