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- PDB-5j7t: Molecular Understanding of USP7 Substrate Recognition and C-Termi... -

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Basic information

Entry
Database: PDB / ID: 5j7t
TitleMolecular Understanding of USP7 Substrate Recognition and C-Terminal Activation
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 / HAUSP / DUB / activation
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 / Ub-specific processing proteases / protein ubiquitination / 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 / molecular replacement / Resolution: 3.2001 Å
AuthorsMurray, J.M. / Rouge, L.
CitationJournal: Structure / Year: 2016
Title: Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation.
Authors: Rouge, L. / Bainbridge, T.W. / Kwok, M. / Tong, R. / Di Lello, P. / Wertz, I.E. / Maurer, T. / Ernst, J.A. / Murray, J.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)77,8641
Polymers77,8641
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.330, 196.730, 226.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-processing protease 7


Mass: 77863.969 Da / Num. of mol.: 1 / Fragment: USP7
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

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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: 3.73 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: PEG 3350, 0.2M tri-potassium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.2→74.245 Å / Num. obs: 19259 / % possible obs: 99.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 84.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.066 / Rrim(I) all: 0.144 / Net I/σ(I): 7.6 / Num. measured all: 91597
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.2-3.21150.671100
14.815-74.2453.60.076171.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8

1nb8


Resolution: 3.2001→47.376 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.56
RfactorNum. reflection% reflection
Rfree0.294 971 5.06 %
Rwork0.2498 --
obs0.2519 19201 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 305.86 Å2 / Biso mean: 127.2596 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.2001→47.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5446 0 0 0 5446
Num. residues----671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025559
X-RAY DIFFRACTIONf_angle_d0.5797515
X-RAY DIFFRACTIONf_chiral_restr0.024807
X-RAY DIFFRACTIONf_plane_restr0.003992
X-RAY DIFFRACTIONf_dihedral_angle_d11.3612118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.36880.38311510.361725772728100
3.3688-3.57980.36241310.34352598272999
3.5798-3.85610.29551420.28742548269099
3.8561-4.24390.31291350.266526122747100
4.2439-4.85750.26571570.235826142771100
4.8575-6.11790.2841260.236126522778100
6.1179-47.38070.2641290.20032629275896
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)
12.4908-0.72341.62826.94492.41599.5732-0.62610.4868-0.3149-0.12570.84860.1120.0463-0.5635-0.21130.68820.01560.16180.62550.19411.1056-24.594616.0877-30.2961
26.86-0.2074-0.58132.65342.3018.2468-0.5368-2.0467-1.13550.89610.6087-0.57051.01491.0558-0.19780.91360.27130.00231.51670.32961.2926-17.379715.6138-16.2685
33.50181.4086-0.96012.27573.14635.8970.3247-1.6341-1.06141.09180.3335-0.41531.04440.7349-0.6661.25930.3152-0.06681.77950.41421.1635-23.384720.3357-2.6692
42.77951.86771.31766.92410.80247.3509-0.0338-0.8448-0.44970.91580.5196-1.0136-0.46020.0124-0.40440.82380.08150.10070.76740.0141.0062-24.673128.3384-17.1754
58.8015-4.1781-1.30545.65193.22033.8627-0.3711-0.1738-0.39120.0941-0.26810.2454-1.1067-1.17780.90740.84750.12050.07811.09620.1890.8524-37.373125.2232-24.5053
62.0863-1.4637-2.2646.18133.03688.70760.1330.0435-0.9368-0.6748-0.0005-0.61160.14280.013-0.40150.6631-0.01010.0210.9017-0.02441.2543-20.664313.4525-36.8305
76.48820.4785-0.19555.1151-0.19392.1674-0.59541.19570.8046-0.38220.4183-0.9095-1.34091.05330.37911.2382-0.393-0.04241.10480.05811.0528-46.8688-27.4341-52.0505
85.74990.11151.58127.13610.19520.6568-0.66860.99971.4164-0.43660.86810.6271-0.51732.02140.35921.3414-0.2581-0.5031.10140.00621.2556-57.8617-22.6909-51.6549
94.51872.45353.14752.8147-1.26619.7672-0.00521.46430.59011.03950.0641-2.2173-0.18141.02710.15011.166-0.3152-0.09281.58830.06611.1532-50.291-26.1915-53.482
109.1363-0.41130.26484.7724-0.95457.7894-0.43790.5008-0.3991-0.60670.3976-0.09420.0827-0.29550.01670.9766-0.0923-0.08150.5248-0.09940.7009-64.8675-41.8506-47.974
111.7516-0.0025-1.27542.71380.51065.12670.4058-0.5487-0.77150.03760.2111-0.3671.02841.4252-0.80261.34210.2571-0.26411.2357-0.03660.9836-52.0691-42.0791-20.3857
122.82921.5484-1.74192.2078-3.09097.85-0.09441.27690.43770.84810.3719-0.5041-0.06911.7928-0.11431.207-0.2803-0.46391.7880.06681.1699-45.2439-31.6571-8.0448
136.4961.1533-2.3024.83570.69882.150.05640.72790.3415-0.43720.06250.0612-0.82880.66660.23541.2040.154-0.29821.7783-0.03450.8843-49.5252-29.2958-13.9768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 211 through 243 )A211 - 243
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 378 )A244 - 378
3X-RAY DIFFRACTION3chain 'A' and (resid 379 through 426 )A379 - 426
4X-RAY DIFFRACTION4chain 'A' and (resid 427 through 469 )A427 - 469
5X-RAY DIFFRACTION5chain 'A' and (resid 470 through 510 )A470 - 510
6X-RAY DIFFRACTION6chain 'A' and (resid 511 through 561 )A511 - 561
7X-RAY DIFFRACTION7chain 'A' and (resid 563 through 627 )A563 - 627
8X-RAY DIFFRACTION8chain 'A' and (resid 628 through 647 )A628 - 647
9X-RAY DIFFRACTION9chain 'A' and (resid 648 through 670 )A648 - 670
10X-RAY DIFFRACTION10chain 'A' and (resid 671 through 770 )A671 - 770
11X-RAY DIFFRACTION11chain 'A' and (resid 771 through 830 )A771 - 830
12X-RAY DIFFRACTION12chain 'A' and (resid 831 through 850 )A831 - 850
13X-RAY DIFFRACTION13chain 'A' and (resid 851 through 881 )A851 - 881

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