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- PDB-5fwi: structure of usp7 catalytic domain and three ubl-domains -

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Basic information

Entry
Database: PDB / ID: 5fwi
Titlestructure of usp7 catalytic domain and three ubl-domains
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
KeywordsHYDROLASE / DEUBIQUITINASE / USP / UBIQUITIN-LIKE
Function / homology
Function and homology information


regulation of telomere capping / histone H2B deubiquitinase activity / histone H2A deubiquitinase activity / regulation of establishment of protein localization to telomere / peptidase complex / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / DNA alkylation repair / deubiquitinase activity / protein K48-linked deubiquitination ...regulation of telomere capping / histone H2B deubiquitinase activity / histone H2A deubiquitinase activity / regulation of establishment of protein localization to telomere / peptidase complex / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / DNA alkylation repair / deubiquitinase activity / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / regulation of tumor necrosis factor-mediated signaling pathway / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / protein K63-linked deubiquitination / negative regulation of gluconeogenesis / protein deubiquitination / ubiquitin ligase complex / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / regulation of signal transduction by p53 class mediator / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / antiviral innate immune response / regulation of protein stability / PML body / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / p53 binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / chromosome / nuclear body / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / Ub-specific processing proteases / cysteine-type endopeptidase activity / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
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 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 C-terminal hydrolase 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKim, R.Q. / van Dijk, W.J. / Sixma, T.K.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structure of Usp7 Catalytic Domain and Three Ubl-Domains Reveals a Connector Alpha-Helix with Regulatory Role.
Authors: Kim, R.Q. / Van Dijk, W.J. / Sixma, T.K.
History
DepositionFeb 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Structure summary
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7


Theoretical massNumber of molelcules
Total (without water)78,8011
Polymers78,8011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.183, 195.040, 219.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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-P ROCESSING PROTEASE 7 / USP7


Mass: 78801.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 207-882
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q93009, ubiquitinyl hydrolase 1

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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: 3.92 Å3/Da / Density % sol: 68.6 % / Description: NONE
Crystal growDetails: 15% PEG 3350 0.2M NA CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97935
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.4→48.76 Å / Num. obs: 17198 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1NB8, 2YLM

1nb8

2ylm


Resolution: 3.4→109.89 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 69.893 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26693 851 4.9 %RANDOM
Rwork0.22221 ---
obs0.22436 16346 99.82 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 171.029 Å2
Baniso -1Baniso -2Baniso -3
1-7.84 Å20 Å20 Å2
2--1.47 Å20 Å2
3----9.3 Å2
Refinement stepCycle: LAST / Resolution: 3.4→109.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 0 0 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195467
X-RAY DIFFRACTIONr_bond_other_d0.0020.025143
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9677386
X-RAY DIFFRACTIONr_angle_other_deg0.925311870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28324.982279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9831529
X-RAY DIFFRACTIONr_chiral_restr0.0710.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216201
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021248
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31310.4682645
X-RAY DIFFRACTIONr_mcbond_other1.31210.4682644
X-RAY DIFFRACTIONr_mcangle_it2.37215.7033301
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.01610.492820
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 70 -
Rwork0.368 1172 -
obs--100 %
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)
12.30190.3043-0.35191.7476-0.08944.9989-0.1962-0.67860.90761.00850.66170.6807-0.1476-0.1777-0.46550.9890.47330.10730.6748-0.21171.0394-29.398180.800389.6967
25.20571.38021.03144.39460.32692.8567-0.36310.2138-0.3193-0.48050.12330.41910.1899-0.14960.23980.2522-0.00830.10120.03870.00210.18346.5931228.711961.9743
36.9586-1.4244-0.39763.23950.2148.6747-0.0609-0.0383-0.1130.09490.08520.29680.4821-0.6596-0.02430.5638-0.11430.30390.70660.04550.2028-4.9012227.044997.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C210 - 554
2X-RAY DIFFRACTION2C555 - 793
3X-RAY DIFFRACTION3C794 - 881

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