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- PDB-4pyz: Crystal structure of the first two Ubl domains of Deubiquitylase USP7 -

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Basic information

Entry
Database: PDB / ID: 4pyz
TitleCrystal structure of the first two Ubl domains of Deubiquitylase USP7
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / Deubiquitylase / ubiquitin-like domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / protein ubiquitination / Ub-specific processing proteases / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsWalker, J.R. / Dong, A. / Ong, M.S. / Dhe-Paganon, S. / Kania, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the first two Ubl domains of Deubiquitylase USP7
Authors: Ong, M.S. / Walker, J.R. / Dong, A. / Dhe-Paganon, S. / Kania, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)63,4674
Polymers63,4672
Non-polymers02
Water21612
1
A: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)31,7341
Polymers31,7341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)31,7343
Polymers31,7341
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.328, 103.755, 116.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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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: 31733.713 Da / Num. of mol.: 2 / Fragment: UNP residues 537-793
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4000, 0.2 M NH4Ac, 0.1 M NaCitrate pH5.6, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.83→50 Å / Num. obs: 19822 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 82.16 Å2 / Rmerge(I) obs: 0.095 / Χ2: 1.109 / Net I/σ(I): 22.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.83-2.886.60.9369580.844199.7
2.88-2.936.70.9019750.889198.8
2.93-2.996.90.729510.905198.7
2.99-3.056.70.5769840.881199.3
3.05-3.116.90.479740.913198.2
3.11-3.196.80.4139520.944199.4
3.19-3.276.80.3379630.943198.3
3.27-3.366.80.2599910.959198.9
3.36-3.456.90.2389631.136198.6
3.45-3.576.90.1679731.035198.3
3.57-3.696.90.1599791.134199.6
3.69-3.846.80.1279951.181199.4
3.84-4.026.80.1069961.201199.8
4.02-4.236.90.0899981.291100
4.23-4.496.90.089931.558199.9
4.49-4.846.90.06610131.3481100
4.84-5.326.90.06110031.2241100
5.32-6.096.70.05810251.0861100
6.09-7.676.90.05210411.091199.9
7.67-506.40.0410951.539198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
BUSTER2.10.0refinement
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YLM

2ylm


Resolution: 2.84→40.71 Å / Cor.coef. Fo:Fc: 0.8741 / Cor.coef. Fo:Fc free: 0.8748 / SU R Cruickshank DPI: 0.768 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 629 3.18 %RANDOM
Rwork0.2438 ---
obs0.2452 19769 98.34 %-
Displacement parametersBiso max: 147.3 Å2 / Biso mean: 80.95 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-37.2332 Å20 Å20 Å2
2--5.6384 Å20 Å2
3----42.8716 Å2
Refine analyzeLuzzati coordinate error obs: 0.564 Å
Refinement stepCycle: LAST / Resolution: 2.84→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 2 12 4076
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1441SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it4179HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion555SEMIHARMONIC5
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_contact4427SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4179HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5682HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion1.82
X-RAY DIFFRACTIONt_other_torsion19.54
LS refinement shellResolution: 2.84→2.99 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3722 74 2.78 %
Rwork0.3198 2585 -
all0.3211 2659 -
obs--98.34 %
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)
11.3183-0.2050.0261.2423-0.31170.6303-0.07070.3199-0.1038-0.1195-0.001-0.09730.21870.0130.07170.0918-0.07120.04090.1879-0.04250.19121.2636-20.567-20.3683
21.3112-0.1888-0.22380.82570.51611.1883-0.05780.09490.3104-0.03780.06160.016-0.18030.0028-0.00380.068-0.0485-0.08250.02680.10790.249344.1291-11.2558-16.5863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|531 - A|793 }A531 - 793
2X-RAY DIFFRACTION2{ B|533 - B|793 }B533 - 793

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