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- PDB-6dgf: Ubiquitin Variant bound to USP2 -

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Basic information

Entry
Database: PDB / ID: 6dgf
TitleUbiquitin Variant bound to USP2
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 2
KeywordsPROTEIN BINDING / Ubiquitin / Deubiquitinase / Ubiquitin Variant
Function / homology
Function and homology information


circadian behavior / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / TNFR1-induced proapoptotic signaling / seminiferous tubule development / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / muscle organ development / entrainment of circadian clock by photoperiod ...circadian behavior / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / TNFR1-induced proapoptotic signaling / seminiferous tubule development / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / muscle organ development / entrainment of circadian clock by photoperiod / locomotor rhythm / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / energy homeostasis / positive regulation of mitotic cell cycle / neuron projection morphogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / regulation of mitochondrial membrane potential / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / cyclin binding / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / 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 signal transduction by p53 class mediator / positive regulation of protein ubiquitination / NF-kB is activated and signals survival / regulation of proteasomal protein catabolic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of innate immune responses to cytosolic DNA / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / circadian regulation of gene expression / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Stabilization of p53
Similarity search - Function
: / 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. / Cysteine proteinases / Cathepsin B; Chain A ...: / 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. / Cysteine proteinases / Cathepsin B; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 2 / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsManczyk, N. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Yeast Two-Hybrid Analysis for Ubiquitin Variant Inhibitors of Human Deubiquitinases.
Authors: Pascoe, N. / Seetharaman, A. / Teyra, J. / Manczyk, N. / Satori, M.A. / Tjandra, D. / Makhnevych, T. / Schwerdtfeger, C. / Brasher, B.B. / Moffat, J. / Costanzo, M. / Boone, C. / Sicheri, F. / Sidhu, S.S.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 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 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 2
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3365
Polymers53,0782
Non-polymers2583
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-37 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.978, 58.093, 46.842
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 2 / 41 kDa ubiquitin-specific protease / Deubiquitinating enzyme 2 / Ubiquitin thioesterase 2 / ...41 kDa ubiquitin-specific protease / Deubiquitinating enzyme 2 / Ubiquitin thioesterase 2 / Ubiquitin-specific-processing protease 2


Mass: 42466.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP2, UBP41 / Production host: Escherichia coli (E. coli) / References: UniProt: O75604, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 10611.225 Da / Num. of mol.: 1 / Mutation: Q2C, K6C, K11R, T12C
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES buffer pH 6, 12% (w/v) PEG3350, 0.2M sodium sulfate

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 18044 / % possible obs: 99 % / Redundancy: 3.2 % / CC1/2: 0.961 / Rsym value: 0.065 / Net I/σ(I): 31.4
Reflection shellResolution: 2.34→2.42 Å / Mean I/σ(I) obs: 8.6 / Num. unique obs: 1628 / Rsym value: 0.149 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 2HD5

1ubq

2hd5


Resolution: 2.34→39.069 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.224 879 4.91 %
Rwork0.1759 --
obs0.1782 17913 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.34→39.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 11 156 3339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023245
X-RAY DIFFRACTIONf_angle_d0.4594399
X-RAY DIFFRACTIONf_dihedral_angle_d25.5731177
X-RAY DIFFRACTIONf_chiral_restr0.038495
X-RAY DIFFRACTIONf_plane_restr0.003569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.48660.31121520.21732678X-RAY DIFFRACTION95
2.4866-2.67860.28631370.20932859X-RAY DIFFRACTION100
2.6786-2.9480.27641510.20632828X-RAY DIFFRACTION99
2.948-3.37440.21691500.18492861X-RAY DIFFRACTION100
3.3744-4.25060.20051450.14762882X-RAY DIFFRACTION100
4.2506-39.07480.18341440.16312926X-RAY DIFFRACTION100

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