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- PDB-4ldt: The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub -

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Basic information

Entry
Database: PDB / ID: 4ldt
TitleThe structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
Components
  • Ubiquitin aldehyde
  • Ubiquitin thioesterase otubain-like
  • Ubiquitin-conjugating enzyme E2 D2
  • Ubiquitin
KeywordsHYDROLASE REGULATOR / isopeptidase / ubiquitin-conjugating / post-translational modification / ubiquitin / ubiquitin-aldehyde
Function / homology
Function and homology information


Ovarian tumor domain proteases / ubiquitin-protein transferase inhibitor activity / negative regulation of double-strand break repair / deNEDDylase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K48-linked deubiquitination / E2 ubiquitin-conjugating enzyme / protein deubiquitination / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination ...Ovarian tumor domain proteases / ubiquitin-protein transferase inhibitor activity / negative regulation of double-strand break repair / deNEDDylase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K48-linked deubiquitination / E2 ubiquitin-conjugating enzyme / protein deubiquitination / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of TORC1 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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-conjugating enzyme E2 D2 / Ubiquitin thioesterase OTUB1 / Ubiquitin thioesterase otubain-like
Similarity search - Component
Biological speciesHomo sapiens (human)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsWiener, R. / DiBello, A.T. / Lombardi, P.M. / Guzzo, C.M. / Zhang, X. / Matunis, M.J. / Wolberger, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1.
Authors: Wiener, R. / Dibello, A.T. / Lombardi, P.M. / Guzzo, C.M. / Zhang, X. / Matunis, M.J. / Wolberger, C.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin thioesterase otubain-like
B: Ubiquitin aldehyde
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0029
Polymers66,7304
Non-polymers2735
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-24 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.894, 131.612, 46.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 4 types, 4 molecules ABCD

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


Mass: 32795.637 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Caenorhabditis elegans (invertebrata)
Gene: OTUB1, OTB1, OTU1, HSPC263, C25D7.8, otub-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FW1, UniProt: Q9XVR6, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin aldehyde


Mass: 8560.831 Da / Num. of mol.: 1
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: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16796.213 Da / Num. of mol.: 1 / Mutation: C85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) / References: UniProt: P62837, ubiquitin-protein ligase
#4: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 321 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING RESIDUES 1-45 OF UNP Q96FW1 AND ...THE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING RESIDUES 1-45 OF UNP Q96FW1 AND RESIDUES 42-284 OF UNP Q9XVR6.

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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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well ...Details: 1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well solution + 10% ethylene glycol, flash frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.901→33.65 Å / Num. all: 51642 / Num. obs: 51582 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.13 / Net I/σ(I): 8.5
Reflection shellResolution: 1.901→1.93 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.57 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DHZ

4dhz


Resolution: 1.901→33.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.665 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22318 2612 5.1 %RANDOM
Rwork0.1918 ---
obs0.19342 48379 98.82 %-
all-51047 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---2.07 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.901→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 17 316 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194626
X-RAY DIFFRACTIONr_bond_other_d0.0020.024400
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9666299
X-RAY DIFFRACTIONr_angle_other_deg0.741310122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04323.578204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64315783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6831534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 177 -
Rwork0.279 3360 -
obs--94.24 %
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)
10.72760.2420.08430.83610.21540.6596-0.0023-0.05870.02110.0293-0.03180.0927-0.0427-0.05760.03410.081-0.0320.01570.1344-0.0150.013117.488827.659815.7155
21.17651.0693-0.22821.8178-0.18951.32280.01440.04570.0595-0.130.06590.0884-0.03730.064-0.08030.1114-0.03780.00050.118-0.01310.009633.469843.7505-0.2706
31.1624-0.1119-0.68661.25860.54192.361-0.02650.02890.047-0.1395-0.0337-0.05720.00320.16180.06020.059-0.02880.00780.08680.02640.015516.16111.4996-6.7362
40.77611.351-0.14263.86381.84963.1631-0.0730.0156-0.30910.09330.4084-0.80590.23190.483-0.33540.06680.0404-0.00570.2393-0.10060.208941.220818.245410.6816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 275
2X-RAY DIFFRACTION2B1 - 76
3X-RAY DIFFRACTION3C0 - 147
4X-RAY DIFFRACTION4D1 - 76

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