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- PDB-4boz: Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4boz
TitleStructure of OTUD2 OTU domain in complex with K11-linked di ubiquitin
Components
  • UBIQUITIN THIOESTERASE OTU1
  • UBIQUITIN-C
KeywordsHYDROLASE
Function / homology
Function and homology information


protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of retrograde protein transport, ER to cytosol / protein K27-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of retrograde protein transport, ER to cytosol / protein K27-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / ERAD pathway / endoplasmic reticulum unfolded protein response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Defective CFTR causes cystic fibrosis
Similarity search - Function
: / OTU1, UBXL domain / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...: / OTU1, UBXL domain / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin thioesterase OTU1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsMevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. ...Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis.
Authors: Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D.
History
DepositionMay 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN THIOESTERASE OTU1
B: UBIQUITIN-C
C: UBIQUITIN-C
D: UBIQUITIN THIOESTERASE OTU1
E: UBIQUITIN-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3157
Polymers67,1315
Non-polymers1842
Water19811
1
A: UBIQUITIN THIOESTERASE OTU1
B: UBIQUITIN-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3693
Polymers29,2772
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-8.4 kcal/mol
Surface area10890 Å2
MethodPISA
2
D: UBIQUITIN THIOESTERASE OTU1
E: UBIQUITIN-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3693
Polymers29,2772
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-9 kcal/mol
Surface area11600 Å2
MethodPISA
3
C: UBIQUITIN-C


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.790, 44.220, 84.950
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UBIQUITIN THIOESTERASE OTU1 / OTUD2 / DUBA-8 / HIV-1-INDUCED PROTEASE 7 / HIN-7 / HSHIN7 / OTU DOMAIN-CONTAINING PROTEIN 2


Mass: 20700.271 Da / Num. of mol.: 2 / Fragment: RESIDUES 132-314 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: Q5VVQ6, ubiquitinyl hydrolase 1
#2: Protein UBIQUITIN-C / UBIQUITIN


Mass: 8576.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: P0CG48
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCATALYTIC CYSTEINE 160 HAD BEEN MUTATED TO ALANINE TO PERMIT COMPLEX FORMATION WITH DI-UBIQUITIN

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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: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE
Crystal growDetails: 0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorDetails: MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. obs: 12691 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 42.89 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.1
Reflection shellResolution: 3.03→3.19 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BOQ

4boq


Resolution: 3.03→43.684 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 613 4.8 %
Rwork0.1933 --
obs0.1964 12689 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→43.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 12 11 4106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094317
X-RAY DIFFRACTIONf_angle_d1.1565866
X-RAY DIFFRACTIONf_dihedral_angle_d14.9311598
X-RAY DIFFRACTIONf_chiral_restr0.072689
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.33480.32151530.22572991X-RAY DIFFRACTION98
3.3348-3.81720.24841500.18832999X-RAY DIFFRACTION98
3.8172-4.80820.21521540.16352988X-RAY DIFFRACTION97
4.8082-43.68880.26811560.2123098X-RAY DIFFRACTION97
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)
13.85210.8850.5014.236-0.24145.26520.56270.85880.13770.14190.34450.4554-0.3421-0.0271-0.79740.68160.10790.05640.60870.11440.474827.4659-10.8947-50.1637
23.0934-1.3643-0.56791.69320.00410.2238-0.08860.14580.1871-0.6369-0.5451-1.27870.21671.42880.40480.56590.09710.29021.12440.33440.778946.0282-9.2844-26.0052
34.3094-1.65180.58162.3328-0.90162.4510.2112-1.1563-0.57050.29450.0958-0.01640.4010.3725-0.24220.4038-0.016-0.07530.54090.11050.454728.9134-4.542411.5888
43.1865-0.6813-0.75712.60420.57981.96120.2113-0.31090.37280.0215-0.01490.0239-0.0104-0.1315-0.1740.2284-0.0348-0.00430.26080.05480.271214.97311.51360.9821
52.5634-0.44970.74493.1945-0.35643.07890.1580.1484-0.1672-0.5364-0.08470.08750.0470.0035-0.03490.34530.0035-0.04020.20450.03220.234624.5781-12.7487-20.3831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C AND ((RESSEQ 1:71))
2X-RAY DIFFRACTION2CHAIN B AND ((RESSEQ 1:76))
3X-RAY DIFFRACTION3CHAIN E AND ((RESSEQ 1:76))
4X-RAY DIFFRACTION4CHAIN D AND ((RESSEQ 146:311))
5X-RAY DIFFRACTION5CHAIN A AND ((RESSEQ 147:308))

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