12ZJ | pdb_000012zj

Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)

• PDB DOI: https://doi.org/10.2210/pdb12ZJ/pdb

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


• Deposited: 2026-04-24 Released: 2026-06-10 
• Deposition Author(s): Korchak, E.J., Bezsonova, I., Hao, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.217 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)

Korchak, E.J., Soriano, G., Semenova, I., Hao, B., Stepihar, D., Bayat, T., Fon Tacer, K., Bezsonova, I.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.24 kDa 
• Atom Count: 4,306 
• Modeled Residue Count: 458 
• Deposited Residue Count: 474 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 7	A, C, E	145	Homo sapiens	Mutation(s): 0  Gene Names: USP7, HAUSP EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens) Explore Q93009  Go to UniProtKB:  Q93009
PHAROS:  Q93009 GTEx:  ENSG00000187555

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAGE-like protein 2	B, D, F	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ55 (Homo sapiens) Explore Q9UJ55  Go to UniProtKB:  Q9UJ55
PHAROS:  Q9UJ55 GTEx:  ENSG00000254585

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.217 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.483	α = 90
b = 50.696	β = 103.78
c = 82.974	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Korchak, E.J., Bezsonova, I., Hao, B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM156397
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R21NS135343

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release