8WMS

Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain

• PDB DOI: https://doi.org/10.2210/pdb8WMS/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: unidentified plasmid
• Mutation(s): No 


• Deposited: 2023-10-04 Released: 2024-07-31 
• Deposition Author(s): Shiraishi, N., Arita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.266 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Starting Model: experimental

Literature

Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain

Shiraishi, N., Arita, K.

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: SAXS

Macromolecule Content

• Total Structure Weight: 12.59 kDa 
• Atom Count: 708 
• Modelled Residue Count: 90 
• Deposited Residue Count: 106 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A	68	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	B	38	Homo sapiens	Mutation(s): 0  Gene Names: DPPA3, STELLAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q6W0C5 (Homo sapiens) Explore Q6W0C5  Go to UniProtKB:  Q6W0C5
PHAROS:  Q6W0C5 GTEx:  ENSG00000187569

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.266 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.802	α = 90
b = 77.802	β = 90
c = 140.674	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Shiraishi, N., Arita, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H02392,
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05741
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05294
Japan Science and Technology	Japan	14530337

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release