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- PDB-4i6l: Crystal structure of OTUB1 in complex with ubiquitin variant -

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Basic information

Entry
Database: PDB / ID: 4i6l
TitleCrystal structure of OTUB1 in complex with ubiquitin variant
Components
  • Ubiquitin
  • Ubiquitin thioesterase OTUB1
KeywordsHYDROLASE / deubiquitinase
Function / homology
Function and homology information


negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / protein deubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants ...negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / protein deubiquitination / 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 / 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 / positive regulation of TORC1 signaling / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / 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 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / PINK1-PRKN Mediated Mitophagy / 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 / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Degradation of DVL / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / EGFR downregulation / Activation of NF-kappaB in B cells / Termination of translesion DNA synthesis
Similarity search - Function
Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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 / Phosphorylase Kinase; domain 1 / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin thioesterase OTUB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.488 Å
AuthorsJuang, Y.C. / Sicheri, F.
CitationJournal: Science / Year: 2013
Title: A strategy for modulation of enzymes in the ubiquitin system.
Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / ...Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / Juang, Y.C. / Landry, M.C. / Yeh, C. / Zeqiraj, E. / Karamboulas, K. / Allali-Hassani, A. / Vedadi, M. / Tyers, M. / Moffat, J. / Sicheri, F. / Pelletier, L. / Durocher, D. / Raught, B. / Rotin, D. / Yang, J. / Moran, M.F. / Dhe-Paganon, S. / Sidhu, S.S.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 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 thioesterase OTUB1
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)35,3332
Polymers35,3332
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-8 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.444, 109.069, 73.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ubiquitin thioesterase OTUB1 / Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / ...Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / Otubain-1 / hOTU1 / Ubiquitin-specific-processing protease OTUB1


Mass: 26572.781 Da / Num. of mol.: 1 / Fragment: UNP residues 45-271 / Mutation: C91S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB1, OTB1, OTU1, HSPC263 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FW1, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin / Ubiquitin


Mass: 8760.101 Da / Num. of mol.: 1 / Fragment: UNP residues 77-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, and 20% (w/v) PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 13269 / Num. obs: 12681 / Observed criterion σ(I): 2.4
Reflection shellResolution: 2.59→2.69 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zfy, 1ubq

2zfy

1ubq


Resolution: 2.488→46.222 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 25.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 580 4.75 %RANDOM
Rwork0.2197 ---
obs0.2218 12212 91.52 %-
all-12681 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.123 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9516 Å20 Å20 Å2
2---2.2483 Å2-0 Å2
3----0.7033 Å2
Refinement stepCycle: LAST / Resolution: 2.488→46.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 0 84 2479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032444
X-RAY DIFFRACTIONf_angle_d0.7153288
X-RAY DIFFRACTIONf_dihedral_angle_d13.329925
X-RAY DIFFRACTIONf_chiral_restr0.053361
X-RAY DIFFRACTIONf_plane_restr0.003420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4877-2.73810.30261180.26672133X-RAY DIFFRACTION69
2.7381-3.13420.32321590.25883065X-RAY DIFFRACTION98
3.1342-3.94840.25311620.21873148X-RAY DIFFRACTION100
3.9484-46.230.24011410.19433286X-RAY DIFFRACTION99
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)
11.40480.0217-0.73670.45370.78551.7878-0.25280.37240.7957-0.4403-0.06670.2119-1.6882-0.2540.58521.02230.1146-0.3390.43170.00830.51882.3726-16.8023-3.8112
21.43820.25220.32232.03511.54032.6274-0.08130.01980.01450.0002-0.12740.2503-0.062-0.07290.13930.0342-0.0293-0.02880.044-0.01150.10111.7043-36.54359.2864
31.98261.08770.07733.03641.5423.0661-0.06680.06340.0007-0.3599-0.06090.1775-0.66190.17840.10460.1834-0.0571-0.04040.0973-0.00840.134216.2813-22.773212.8918
44.32585.30664.15128.6335.95854.3369-0.41340.6132-0.3085-0.65150.5048-0.6784-0.11910.118-0.2120.4132-0.02690.10790.1719-0.04490.250734.2242-7.274816.7792
50.9809-0.4821-0.4521.3304-1.07881.7562-0.4120.3207-0.433-1.00040.5711-0.51490.06920.07240.16050.4294-0.13350.15490.2192-0.07170.267430.9758-10.491712.8027
64.7367-2.19230.12491.64610.74799.4759-0.12710.14660.0023-0.78120.226-0.8336-0.4394-0.0839-0.06340.3047-0.0231-0.00870.1112-0.06080.311932.1223.611621.0953
72.2849-0.195-0.06034.94692.95361.76490.09340.56340.1559-1.2731-0.0723-0.0065-0.74170.01360.09480.368-0.0314-0.01280.17210.0150.114425.8169-1.588212.6243
81.2334-1.44380.06563.49790.47625.4231-0.2430.2490.0128-0.94030.08610.8034-0.021-1.12080.12740.3092-0.1115-0.14890.3347-0.03080.366119.3449-6.125114.5033
94.55483.4189-3.74215.4037-6.00667.02140.2431-0.07080.49940.14620.25920.8586-0.0363-0.8247-0.34440.2103-0.0535-0.02090.2572-0.04610.211823.8809-4.761626.339
103.9820.31380.79042.10891.00134.3759-0.0642-0.4729-0.1779-0.16050.0153-0.7548-0.28350.4958-0.11420.1784-0.1074-0.01280.23870.06040.274133.7687-4.241926.4265
113.13271.80161.77687.99520.82568.5766-0.19720.04160.2703-0.68650.19370.2096-0.0924-0.54780.13090.2519-0.11410.01290.19290.0080.173522.4677-11.549817.5928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 43:76)
2X-RAY DIFFRACTION2chain 'A' and (resseq 77:185)
3X-RAY DIFFRACTION3chain 'A' and (resseq 186:271)
4X-RAY DIFFRACTION4chain 'B' and (resseq -1:7)
5X-RAY DIFFRACTION5chain 'B' and (resseq 8:17)
6X-RAY DIFFRACTION6chain 'B' and (resseq 18:22)
7X-RAY DIFFRACTION7chain 'B' and (resseq 23:34)
8X-RAY DIFFRACTION8chain 'B' and (resseq 35:44)
9X-RAY DIFFRACTION9chain 'B' and (resseq 45:56)
10X-RAY DIFFRACTION10chain 'B' and (resseq 57:65)
11X-RAY DIFFRACTION11chain 'B' and (resseq 66:73)

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