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- PDB-12zj: Crystal structure of USP7 TRAF domain in complex with MAGEL2 pept... -

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Basic information

Entry
Database: PDB / ID: 12zj
TitleCrystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
Components
  • MAGE-like protein 2
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsPEPTIDE BINDING PROTEIN / Deubiquitinase TRAF domain Complex Ubiquitin signaling
Function / homology
Function and homology information


Arp2/3 complex-mediated actin nucleation / regulation of telomere capping / positive regulation of actin nucleation / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / : / DNA alkylation repair / K48-linked deubiquitinase activity ...Arp2/3 complex-mediated actin nucleation / regulation of telomere capping / positive regulation of actin nucleation / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / : / DNA alkylation repair / K48-linked deubiquitinase activity / retrograde transport, endosome to Golgi / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gluconeogenesis / protein deubiquitination / protein K63-linked ubiquitination / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / regulation of signal transduction by p53 class mediator / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of protein stability / regulation of circadian rhythm / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / p53 binding / ubiquitin-protein transferase activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / rhythmic process / chromosome / early endosome / cysteine-type deubiquitinase activity / ubiquitinyl hydrolase 1 / endosome / protein stabilization / Ub-specific processing proteases / nuclear body / protein ubiquitination / cysteine-type endopeptidase activity / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal ...MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 7 / MAGE-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsKorchak, E.J. / Bezsonova, I. / Hao, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM156397 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS135343 United States
CitationJournal: To Be Published
Title: Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
Authors: Korchak, E.J. / Soriano, G. / Semenova, I. / Hao, B. / Stepihar, D. / Bayat, T. / Fon Tacer, K. / Bezsonova, I.
History
DepositionApr 24, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: MAGE-like protein 2
C: Ubiquitin carboxyl-terminal hydrolase 7
D: MAGE-like protein 2
E: Ubiquitin carboxyl-terminal hydrolase 7
F: MAGE-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,24411
Polymers54,9196
Non-polymers3255
Water8,503472
1
A: Ubiquitin carboxyl-terminal hydrolase 7
B: MAGE-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6317
Polymers18,3062
Non-polymers3255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin carboxyl-terminal hydrolase 7
D: MAGE-like protein 2


Theoretical massNumber of molelcules
Total (without water)18,3062
Polymers18,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ubiquitin carboxyl-terminal hydrolase 7
F: MAGE-like protein 2


Theoretical massNumber of molelcules
Total (without water)18,3062
Polymers18,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.483, 50.696, 82.974
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 16986.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Plasmid: pET28b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide MAGE-like protein 2 / Necdin-like protein 1 / Protein nM15


Mass: 1319.402 Da / Num. of mol.: 3 / Fragment: 968-980 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJ55
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 250mM MgCl2 100mM Tris 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920208 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920208 Å / Relative weight: 1
ReflectionResolution: 1.628→41.5 Å / Num. obs: 58428 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 23.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.092 / Rrim(I) all: 0.145 / Rsym value: 0.112 / Net I/σ(I): 6.4
Reflection shellResolution: 1.628→1.656 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.588 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2903 / CC1/2: 0.345 / Rpim(I) all: 1.331 / Rrim(I) all: 2.082 / Rsym value: 1.588 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→41.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2853 4.99 %RANDOM
Rwork0.194 ---
obs0.195 57208 97.8 %-
Displacement parametersBiso mean: 34.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.8974 Å20 Å22.3552 Å2
2---3.6197 Å20 Å2
3---0.7222 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.63→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 20 472 4263
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015378HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1777SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes675HARMONIC5
X-RAY DIFFRACTIONt_it3962HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.61
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4783SEMIHARMONIC4
LS refinement shellResolution: 1.63→1.64 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2586 -5.41 %
Rwork0.2515 1083 -
all0.2519 1145 -
obs--79.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2735-0.04940.10810.43350.03270.7433-0.00430.21840.01280.0247-0.0350.03250.0152-0.04120.0393-0.03340.00390.0096-0.03910.008-0.021320.816511.2122-12.9723
21.515-0.4058-0.02371.2865-0.21251.09290.0358-0.04170.14710.0055-0.01960.0735-0.1701-0.0632-0.0162-0.05110.00860.0081-0.0533-0.0005-0.04229.57793.354713.0142
31.0052-0.82621.7141.0569-1.05952.9442-0.08850.24840.08160.1661-0.129-0.0546-0.1070.62130.2175-0.176-0.0193-0.01390.16840.126-0.21056.9587-15.004640.2135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ E|* }

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