8XV4

Crystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)

• PDB DOI: https://doi.org/10.2210/pdb8XV4/pdb

• Classification: GENE REGULATION/INHIBITOR
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-14 Released: 2024-11-06 
• Deposition Author(s): Du, X., Gan, Q., Xu, J., Liu, J.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Crystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)

Du, X., Gan, Q., Xu, J., Liu, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 61.97 kDa 
• Atom Count: 4,029 
• Modelled Residue Count: 493 
• Deposited Residue Count: 528 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A, B	229	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Developmental pluripotency-associated protein 3	C, D	35	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q8QZY3 (Mus musculus) Explore Q8QZY3  Go to UniProtKB:  Q8QZY3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.713	α = 90
b = 72.365	β = 108.05
c = 63.065	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Du, X., Gan, Q., Xu, J., Liu, J.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2022YFA1303101

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release