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- PDB-5jtj: USP7CD-CTP in complex with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5jtj
TitleUSP7CD-CTP in complex with Ubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 7,Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 / HAUSP / C-terminal activation
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 / : / K48-linked deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...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 / : / K48-linked deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / symbiont-mediated disruption of host cell PML body / : / female gonad development / seminiferous tubule development / negative regulation of gene expression via chromosomal CpG island methylation / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of gluconeogenesis / energy homeostasis / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / regulation of neuron apoptotic process / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / Pexophagy / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / positive regulation of protein ubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of CDH1 / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Degradation of CRY and PER proteins / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1
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 / molecular replacement / Resolution: 3.321 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
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 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 / 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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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,Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3683
Polymers53,3282
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-9 kcal/mol
Surface area18940 Å2
MethodPISA
2
A: Ubiquitin carboxyl-terminal hydrolase 7,Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 7,Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 7,Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 7,Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,47412
Polymers213,3138
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area22440 Å2
ΔGint-128 kcal/mol
Surface area67910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.060, 148.060, 179.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1201-

CA

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7,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: 44751.527 Da / Num. of mol.: 1
Fragment: UNP residues 193-538 LINKED via GGSGG to Residues 1084-1102
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: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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: 5.34 Å3/Da / Density % sol: 76.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.321→74.03 Å / Num. obs: 17846 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 106.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.041 / Rrim(I) all: 0.19 / Net I/σ(I): 18.1 / Num. measured all: 377723
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.321-3.33221.81.881199.5
15.41-179.94613.40.0571100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1nbf


Resolution: 3.321→74.03 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 19.83
RfactorNum. reflection% reflection
Rfree0.2088 939 5.28 %
Rwork0.1911 --
obs0.1921 17795 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 243.8 Å2 / Biso mean: 111.4424 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.321→74.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 1 0 3480
Biso mean--148.15 --
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093532
X-RAY DIFFRACTIONf_angle_d0.964765
X-RAY DIFFRACTIONf_chiral_restr0.051523
X-RAY DIFFRACTIONf_plane_restr0.005621
X-RAY DIFFRACTIONf_dihedral_angle_d15.7892147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.321-3.49570.3391420.292123352477
3.4957-3.71470.25191230.235823602483
3.7147-4.00150.24691350.215723692504
4.0015-4.40420.16731420.173723632505
4.4042-5.04140.18271280.159523962524
5.0414-6.35110.20741190.190924472566
6.3511-74.04840.19611500.180325862736
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)
14.18170.6494-1.7533.5722-1.37884.6190.2276-0.357-0.03560.8183-0.4124-0.524-1.04970.635101.5272-0.325-0.25030.80280.06680.8669-53.995931.2832-7.5328
22.43811.4626-1.00723.2534-1.6164.4438-0.39140.1106-0.6259-0.0405-0.081-0.60670.34680.0839-01.1243-0.10740.00680.67430.02421.177-58.343811.0575-16.1984
30.1936-0.1048-0.7781.93670.34712.4404-1.1799-0.19180.91030.28020.1987-0.2343-1.93460.44010.00032.2191-0.3069-0.3641.05980.11151.1195-55.696241.1068-4.7405
40.3834-0.2269-0.49860.1680.33780.6919-0.41630.88580.0273-0.07750.3510.76950.2751-0.2087-0.00011.3676-0.42120.00091.1475-0.06130.964-71.187118.4421-32.6871
50.38590.2154-0.04670.1099-0.01770.3133-0.1420.03240.2068-0.03850.37480.6632-0.0806-0.745-0.00011.2955-0.2152-0.00631.05670.10110.9307-76.314621.8839-24.6466
60.0243-0.05940.00440.1335-0.06620.1343-0.779-0.11231.05530.2020.3785-0.1134-1.34520.11590.00021.237-0.23990.02890.9804-0.03550.9352-65.692928.8099-25.3893
71.391-0.4240.72781.0709-0.58360.5209-0.55980.7339-0.1699-0.22190.5913-0.4888-0.1908-1.0711-0.00031.1483-0.161-0.02460.8264-0.10570.8566-66.613722.5028-26.0284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 209 through 325 )A209 - 325
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 537 )A326 - 537
3X-RAY DIFFRACTION3chain 'A' and (resid 538 through 1102 )A538 - 1102
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 22 )B1 - 22
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 44 )B23 - 44
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 55 )B45 - 55
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 76 )B56 - 76

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