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- PDB-4bos: Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linke... -

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Basic information

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


negative regulation of retrograde protein transport, ER to cytosol / protein K27-linked deubiquitination / protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity ...negative regulation of retrograde protein transport, ER to cytosol / protein K27-linked deubiquitination / protein K33-linked deubiquitination / protein K29-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 deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / 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 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / macroautophagy / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Peroxisomal protein import / Degradation of AXIN
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
NITRATE ION / Polyubiquitin-C / Ubiquitin thioesterase OTU1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 24, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 31, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_validate_close_contact / struct_conn
Item: _atom_site.occupancy
Revision 2.1Dec 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 THIOESTERASE OTU1
C: POLYUBIQUITIN-C
E: POLYUBIQUITIN-C
F: OTUD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,21311
Polymers56,8785
Non-polymers3346
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.480, 164.480, 44.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11B-1312-

MG

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Components

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Protein , 2 types, 4 molecules ABCE

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


Mass: 19086.428 Da / Num. of mol.: 2 / Fragment: OTU DOMAIN, RESIDUES 147-314 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: Q5VVQ6, ubiquitinyl hydrolase 1
#2: Protein POLYUBIQUITIN-C / OTUD2


Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: P0CG48

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Protein/peptide , 1 types, 1 molecules F

#3: Protein/peptide OTUD2


Mass: 1551.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: P0CG48*PLUS

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Non-polymers , 3 types, 237 molecules

#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATION OF CATALYTIC C160A IN CHAINS A AND B TO PERMIT CO- CRYSTALLISATION WITH UBIQUITIN COMPLEX ...MUTATION OF CATALYTIC C160A IN CHAINS A AND B TO PERMIT CO- CRYSTALLISATION WITH UBIQUITIN COMPLEX ENTRY REFERS TO A SINGLE PROCESSED CHAIN. UBIQUITIN WAS SUBSEQUENTLY MODIFIED WITH A PEPTIDE (CHAIN F) THROUGH AN ISOPEPTIDE LINKAGE FROM IT'S C-TERMINAL GLYCINE TO K11 IN THE PEPTIDE. CHAIN F IS A SYNTHETIC PEPTIDE THAT CORRESPOND TO RESIDUES WITHIN UBIQUITIN THAT HAVE BEEN CHEMICALLY LINKED TO UBIQUITIN CHAINS C AND E C-TERMINUS, THROUGH THE PEPTIDE LYS11 NH2 GROUP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.1 % / Description: NONE
Crystal growDetails: 21% PEG 3,350, 100 MM SODIUM ACETATE, 200 MM MAGNESIUM NITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→53.84 Å / Num. obs: 29294 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 37.15 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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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: 2.35→44.73 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 25.03 / Stereochemistry target values: ML
Details: THE C-TERMINUS OF CHAIN C IS LINKED THROUGH AN ISOPEPTIDE BOND TO LYS11 OF CHAIN F AND HAS BEEN REFINED AS SUCH LINKAGE.
RfactorNum. reflection% reflection
Rfree0.2379 1487 5.1 %
Rwork0.1867 --
obs0.1892 29281 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 21 231 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093871
X-RAY DIFFRACTIONf_angle_d1.1395275
X-RAY DIFFRACTIONf_dihedral_angle_d14.3151426
X-RAY DIFFRACTIONf_chiral_restr0.073616
X-RAY DIFFRACTIONf_plane_restr0.005694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.42590.35561420.27762456X-RAY DIFFRACTION100
2.4259-2.51260.30861430.25372495X-RAY DIFFRACTION100
2.5126-2.61320.30421260.24452533X-RAY DIFFRACTION100
2.6132-2.73210.2971460.21632475X-RAY DIFFRACTION100
2.7321-2.87610.28691250.20472514X-RAY DIFFRACTION100
2.8761-3.05620.27451240.21052530X-RAY DIFFRACTION100
3.0562-3.29210.24091380.20042517X-RAY DIFFRACTION100
3.2921-3.62330.23251230.17452537X-RAY DIFFRACTION100
3.6233-4.14730.21511430.15322548X-RAY DIFFRACTION100
4.1473-5.22390.16541360.14542535X-RAY DIFFRACTION100
5.2239-44.73810.22871410.18682654X-RAY DIFFRACTION100

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