12ZJ: USP7 TRAF domain

Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980). Determined by X-ray diffraction at 1.63 Å resolution. Released 10 Jun 2026.

Method: X-ray diffraction
Resolution: 1.63 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,306
Mol. weight: 55.24 kDa
Ligands: MG
Released: 10 Jun 2026

Explore 12ZJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

12ZJ contains 17 α-helices and 43 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	68-75	8	1
α-helix	78-80	3
β-strand	85-86	2	2
α-helix	87-89	3
β-strand	90-92	3	2
β-strand	95-104	10	2
β-strand	114-121	8	2
β-strand	131-140	10	1
α-helix	146-148	3
β-strand	150-159	10	1
β-strand	162	1	1
β-strand	164-172	9	2
α-helix	173-176	4
β-strand	185	1	3
β-strand	188	1	3
β-strand	189-197	9	1
α-helix	198-200	3
β-strand	201	1	1

Chains B and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	974	1	2

Chain C: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	63-65	3
β-strand	68-75	8	4
α-helix	78-80	3
β-strand	85-86	2	5
α-helix	87-89	3
β-strand	90-92	3	5
β-strand	95-106	12	5
β-strand	109-121	13	5
β-strand	131-140	10	4
α-helix	146-148	3
β-strand	150-159	10	4
β-strand	162	1	4
β-strand	164-172	9	5
α-helix	173-176	4
β-strand	185	1	6
β-strand	188	1	6
β-strand	189-197	9	4
α-helix	198-200	3
β-strand	201	1	4

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	969-971	3
β-strand	974	1	5

Chain E: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	68-75	8	7
α-helix	78-80	3
β-strand	85-86	2	8
α-helix	87-89	3
β-strand	90-92	3	9
β-strand	95-97	3	9
β-strand	98-105	8	8
β-strand	113-120	8	8
β-strand	131-140	10	7
α-helix	146-148	3
β-strand	150-159	10	7
β-strand	162	1	7
β-strand	164-172	9	8
α-helix	173-176	4
β-strand	185	1	10
β-strand	188	1	10
β-strand	189-197	9	7
α-helix	198-200	3
β-strand	201	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	A, C, E	protein	145	Homo sapiens	Q93009 (AlphaFold model)
MAGE-like protein 2	B, D, F	protein	13	Homo sapiens	Q9UJ55 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>12ZJ_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains A, C, E)
GDTSWRSEATFQFTVERFSRLSESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQ
CNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPE
KGFIDDDKVTFEVFVQADAPHGVAW

Sequence of entity 2 (B, D, F), FASTA

>12ZJ_2 MAGE-like protein 2 (chains B, D, F)
SAWEGPSTSRALG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980). Korchak, E.J., Soriano, G., Semenova, I. et al. To be published.

Other PDB entries of the same protein (UniProt Q93009 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YSI 1.02 Å, Structure of USP7 with a novel viral protein
5KYC 1.43 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin…
5KYF 1.45 Å, Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin
2FOJ 1.6 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with p53 peptide…
2XXN 1.6 Å, Structure of the vIRF4-HAUSP TRAF domain complex
5KYD 1.62 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin
2F1W 1.65 Å, Crystal structure of the TRAF-like domain of HAUSP/USP7
1YY6 1.7 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1…
2F1Y 1.7 Å, Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide
4KG9 1.7 Å, Crystal Structure Of USP7-NTD with MCM-BP
5N9T 1.73 Å, Crystal structure of USP7 in complex with a potent, selective and reversible…
9DEM 1.77 Å, USP7 in complex with macrocycle MC04

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