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- PDB-4dhi: Structure of C. elegans OTUB1 bound to human UBC13 -

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Basic information

Entry
Database: PDB / ID: 4dhi
TitleStructure of C. elegans OTUB1 bound to human UBC13
Components
  • Ubiquitin thioesterase otubain-like
  • Ubiquitin-conjugating enzyme E2 N
KeywordsHYDROLASE/LIGASE / ubiquitin E2 enzyme fold / ubiquitination / HYDROLASE-LIGASE complex
Function / homology
Function and homology information


Ovarian tumor domain proteases / : / UBC13-UEV1A complex / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination / protein K48-linked deubiquitination / postreplication repair ...Ovarian tumor domain proteases / : / UBC13-UEV1A complex / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination / protein K48-linked deubiquitination / postreplication repair / positive regulation of intracellular signal transduction / positive regulation of double-strand break repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / regulation of DNA repair / ubiquitin ligase complex / negative regulation of TORC1 signaling / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of DNA repair / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / Aggrephagy / FCERI mediated NF-kB activation / Interleukin-1 signaling / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of NF-kappaB transcription factor activity / Processing of DNA double-strand break ends / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / proteolysis / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Papain-like cysteine peptidase superfamily / Phosphorylase Kinase; domain 1 / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / Ubiquitin thioesterase otubain-like
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWiener, R. / Zhang, X. / Wang, T. / Wolberger, C.
CitationJournal: Nature / Year: 2012
Title: The mechanism of OTUB1-mediated inhibition of ubiquitination.
Authors: Wiener, R. / Zhang, X. / Wang, T. / Wolberger, C.
History
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Mar 14, 2012Group: Database references
Revision 1.3Apr 4, 2012Group: Database references
Revision 1.4Sep 13, 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

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin thioesterase otubain-like
D: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)49,4802
Polymers49,4802
Non-polymers00
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-10 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.070, 111.070, 179.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11D-320-

HOH

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Components

#1: Protein Ubiquitin thioesterase otubain-like / OTUB1 / Deubiquitinating enzyme otubain-like / Ubiquitin-specific-processing protease otubain-like


Mass: 32322.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: otub-1, C25D7.8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XVR6, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin-conjugating enzyme E2 N / Ubc13 / Bendless-like ubiquitin-conjugating enzyme / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17157.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli) / References: UniProt: P61088, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 1 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.034 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034 Å / Relative weight: 1
ReflectionResolution: 1.8→41 Å / Num. all: 61151 / Num. obs: 61151 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
REFMAC5.5.0109refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1J7D and 2ZFY

1j7d

2zfy


Resolution: 1.8→40.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.208 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20866 3084 5.1 %RANDOM
Rwork0.18673 ---
obs0.18782 57931 99.82 %-
all-61151 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.876 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 374 3489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223238
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9634408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28823.885157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48415549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9981523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212493
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9071.51961
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76423182
X-RAY DIFFRACTIONr_scbond_it2.4331277
X-RAY DIFFRACTIONr_scangle_it4.1664.51220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 214 -
Rwork0.239 4202 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 24.8727 Å / Origin y: 37.3876 Å / Origin z: -26.871 Å
111213212223313233
T0.0682 Å20.0368 Å20.0003 Å2-0.0305 Å2-0.0072 Å2--0.0451 Å2
L0.0872 °2-0.0216 °20.0815 °2-0.1549 °2-0.0673 °2--0.1943 °2
S0.025 Å °0.0025 Å °-0.0192 Å °-0.0549 Å °-0.0189 Å °0.0435 Å °0.0501 Å °0.0026 Å °-0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B38 - 275
2X-RAY DIFFRACTION1D3 - 152

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