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- PDB-5kyd: Crystal structure of USP7 catalytic domain [V302K] mutant in comp... -

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Basic information

Entry
Database: PDB / ID: 5kyd
TitleCrystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 catalytic domain / deubiquitinase / V302K mutant / ubiquitin
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 / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked deubiquitinase activity / protein deubiquitination / female meiosis I ...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 / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked deubiquitinase activity / protein deubiquitination / female meiosis I / positive regulation of protein monoubiquitination / symbiont-mediated disruption of host cell PML body / mitochondrion transport along microtubule / fat pad development / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of gluconeogenesis / transcription-coupled nucleotide-excision repair / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / neuron projection morphogenesis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of signal transduction by p53 class mediator / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation
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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsRouge, L. / Ozen, A.
CitationJournal: Structure / Year: 2018
Title: Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation.
Authors: Ozen, A. / Rouge, L. / Bashore, C. / Hearn, B.R. / Skelton, N.J. / Dueber, E.C.
History
DepositionJul 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Polyubiquitin-B
A: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)49,1952
Polymers49,1952
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-1 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.050, 80.470, 86.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: 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: 40617.930 Da / Num. of mol.: 1 / Fragment: UNP residues 192-538 / Mutation: V302K
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M Ammonium fluoride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→27.16 Å / Num. obs: 55856 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 22.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.625-1.645.70.9970.562193.8
8.7-27.166.10.0440.997197

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Processing

Software
NameVersionClassification
MOSFLM7.1.1data reduction
Aimless0.5.1data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
PHASER1.10.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8, 1UBQ

1nb8

1ubq


Resolution: 1.62→27.16 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.2133 2013 3.61 %
Rwork0.1742 --
obs0.1756 55790 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.3 Å2 / Biso mean: 29.9042 Å2 / Biso min: 12.99 Å2
Refinement stepCycle: final / Resolution: 1.62→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 381 3753
Biso mean---37.2 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063483
X-RAY DIFFRACTIONf_angle_d0.8664705
X-RAY DIFFRACTIONf_chiral_restr0.059511
X-RAY DIFFRACTIONf_plane_restr0.006618
X-RAY DIFFRACTIONf_dihedral_angle_d16.2562130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6162-1.65660.32251410.28533602374395
1.6566-1.70140.2841470.257138193966100
1.7014-1.75140.27241410.241438503991100
1.7514-1.80790.24671430.221937843927100
1.8079-1.87250.25551450.21313821396699
1.8725-1.94750.22781260.196238363962100
1.9475-2.03610.20911500.18838013951100
2.0361-2.14340.23861490.18073826397599
2.1434-2.27760.20111470.171438313978100
2.2776-2.45340.22351350.177238453980100
2.4534-2.70010.23321450.178138754020100
2.7001-3.09030.19771470.174838864033100
3.0903-3.89160.1851420.153939324074100
3.8916-27.1640.20011550.14914069422499
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)
14.32551.63742.05583.85861.65393.90610.2024-0.59060.29350.4728-0.32940.11-0.02940.2880.14870.2768-0.0628-0.0010.3121-0.05060.1833-6.2296-12.487918.2987
22.82141.3039-1.85493.779-1.76126.1820.18430.39260.2871-0.3129-0.07830.5914-0.03720.399-0.12140.2321-0.0024-0.03410.3107-0.0430.2555-10.0435-10.6129.0174
36.29590.042-0.03535.31250.88633.07650.08290.29260.5416-0.0172-0.10990.4756-0.13950.10720.02690.2006-0.0045-0.01010.18050.00130.2713-7.8615-3.210111.9885
41.4744-1.5909-1.13395.31552.08761.9051-0.0662-0.14060.69990.25430.2071-0.4822-0.20550.2137-0.12460.2327-0.0147-0.00960.2115-0.03530.3299-0.4589-1.45115.4027
52.2574-0.13241.43843.574-1.59123.2484-0.07040.73440.3489-0.42030.1123-0.4133-0.36980.3653-0.08250.3322-0.03620.04660.27270.02360.23733.3142-9.15256.4357
65.2183.1563-4.21634.1674-3.98264.342-0.30630.7256-0.2683-0.59940.3064-0.2180.18270.13150.03940.2806-0.06870.04330.2964-0.05930.1637-3.7224-16.3055.7885
73.73084.18561.68964.66471.86840.7561-0.0554-0.11410.39030.106-0.05260.175-0.33840.17380.07970.3075-0.0555-0.03860.2395-0.01280.23943.7018-4.048318.0933
81.5397-0.1507-0.24852.40340.871.8827-0.01860.23990.0442-0.25010.0445-0.1737-0.20930.0216-0.01720.1974-0.0030.02560.2132-0.00950.167825.2225-5.791111.0709
92.76141.0642-0.58160.4735-0.45140.1008-0.10720.0574-0.2472-0.09280.056-0.03490.10180.05210.05530.17640.00680.01180.1802-0.04370.17584.2398-23.576512.6605
101.69120.39070.36830.2343-0.12980.2081-0.0304-0.2523-0.00110.0502-0.03580.0608-0.0087-0.0510.05360.20060.02190.0220.2005-0.02360.1945-2.6711-19.876924.5084
111.93390.83730.39031.69920.2751.1075-0.0021-0.33980.03410.2325-0.0284-0.0299-0.063-0.13040.00150.17030.0439-0.01310.171-0.01020.088718.3784-12.585829.5761
121.93070.0969-0.50081.6436-0.97362.7590.02070.7212-0.1212-0.33570.0159-0.6261-0.06190.50730.11620.2655-0.06220.16510.5203-0.04580.356237.029-11.28923.052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 11 )D1 - 11
2X-RAY DIFFRACTION2chain 'D' and (resid 12 through 22 )D12 - 22
3X-RAY DIFFRACTION3chain 'D' and (resid 23 through 34 )D23 - 34
4X-RAY DIFFRACTION4chain 'D' and (resid 35 through 44 )D35 - 44
5X-RAY DIFFRACTION5chain 'D' and (resid 45 through 55 )D45 - 55
6X-RAY DIFFRACTION6chain 'D' and (resid 56 through 65 )D56 - 65
7X-RAY DIFFRACTION7chain 'D' and (resid 66 through 76 )D66 - 76
8X-RAY DIFFRACTION8chain 'A' and (resid 210 through 309 )A210 - 309
9X-RAY DIFFRACTION9chain 'A' and (resid 310 through 348 )A310 - 348
10X-RAY DIFFRACTION10chain 'A' and (resid 349 through 400 )A349 - 400
11X-RAY DIFFRACTION11chain 'A' and (resid 401 through 527 )A401 - 527
12X-RAY DIFFRACTION12chain 'A' and (resid 528 through 550 )A528 - 550

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