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- PDB-4m5w: Crystal structure of the USP7/HAUSP catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4m5w
TitleCrystal structure of the USP7/HAUSP catalytic domain
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / Ubiquitin-specific cysteine protease
Function / homology
Function and homology information


regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation ...regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of gluconeogenesis / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of circadian rhythm / regulation of protein stability / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / p53 binding / rhythmic process / Regulation of TP53 Degradation / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / nuclear body / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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. ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsMolland, K.L. / Mesecar, A.D. / Zhou, Q.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: A 2.2 angstrom resolution structure of the USP7 catalytic domain in a new space group elaborates upon structural rearrangements resulting from ubiquitin binding.
Authors: Molland, K. / Zhou, Q. / Mesecar, A.D.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4685
Polymers41,1481
Non-polymers3204
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.312, 69.193, 75.726
Angle α, β, γ (deg.)90.00, 131.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / USP7 / HAUSP / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / ...USP7 / HAUSP / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 41148.473 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 207-560)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 22% PEG3350, 0.2 M sodium bromide, 0.15 mM Cymal-7, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.244→56.904 Å / Num. all: 18890 / Num. obs: 17493 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.9
Reflection shellResolution: 2.244→2.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.1 / % possible all: 66.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NB8

1nb8


Resolution: 2.244→38.441 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 899 5.14 %
Rwork0.1856 --
obs0.1884 17493 91.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.244→38.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 4 89 2881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072847
X-RAY DIFFRACTIONf_angle_d1.113839
X-RAY DIFFRACTIONf_dihedral_angle_d15.7761081
X-RAY DIFFRACTIONf_chiral_restr0.075409
X-RAY DIFFRACTIONf_plane_restr0.004503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.244-2.38490.34771080.26551989X-RAY DIFFRACTION66
2.3849-2.5690.30491440.25612562X-RAY DIFFRACTION85
2.569-2.82740.33411520.22962951X-RAY DIFFRACTION99
2.8274-3.23640.29271700.19993005X-RAY DIFFRACTION100
3.2364-4.07680.22581630.16783028X-RAY DIFFRACTION100
4.0768-38.44670.19271620.16183059X-RAY DIFFRACTION99
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)
13.2359-0.93630.83662.31590.10684.1471-0.2639-0.7303-0.4231-0.09940.22260.01070.45640.7021-0.03940.36060.19150.02240.73560.10250.254365.660233.981669.8265
21.68122.2548-2.20684.0141-3.13485.42380.0941-0.15690.04120.67670.28750.6731-0.0149-0.0034-0.28760.39110.13540.07790.64580.05130.420444.464640.934195.2029
31.6591-1.39810.10424.3942-0.84246.20390.2428-0.62990.1357-0.0693-0.06860.5317-0.0081-0.3225-0.17120.20850.0450.03020.5197-0.01140.299650.33748.981179.4345
42.097-0.275-2.55673.72610.91442.46360.1459-0.50310.2135-0.30710.1374-0.2704-0.21391.1686-0.06260.18120.0463-0.07540.9514-0.04490.249365.815346.786272.7771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 208 through 325 )
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 397 )
3X-RAY DIFFRACTION3chain 'A' and (resid 398 through 436 )
4X-RAY DIFFRACTION4chain 'A' and (resid 437 through 554 )

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