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- PDB-4dhj: The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex -

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Basic information

Entry
Database: PDB / ID: 4dhj
TitleThe structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex
Components
  • Ubiquitin aldehyde
  • Ubiquitin thioesterase otubain-like
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin
KeywordsHYDROLASE/SIGNALING PROTEIN/LIGASE / ubiquitination / HYDROLASE-SIGNALING PROTEIN-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 / 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 TORC1 signaling / 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 DNA repair / 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 BACH1 activity / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / Degradation of DVL / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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
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 N / Ubiquitin thioesterase otubain-like
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin thioesterase otubain-like
B: Ubiquitin aldehyde
E: Ubiquitin thioesterase otubain-like
F: Ubiquitin aldehyde
D: Ubiquitin
C: Ubiquitin-conjugating enzyme E2 N
I: Ubiquitin thioesterase otubain-like
J: Ubiquitin aldehyde
K: Ubiquitin-conjugating enzyme E2 N
G: Ubiquitin-conjugating enzyme E2 N
L: Ubiquitin thioesterase otubain-like
M: Ubiquitin aldehyde
H: Ubiquitin
N: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)249,40814
Polymers249,40814
Non-polymers00
Water5,567309
1
A: Ubiquitin thioesterase otubain-like
B: Ubiquitin aldehyde
C: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)58,0413
Polymers58,0413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-19 kcal/mol
Surface area22810 Å2
MethodPISA
2
E: Ubiquitin thioesterase otubain-like
F: Ubiquitin aldehyde
G: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)58,0413
Polymers58,0413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-16 kcal/mol
Surface area22440 Å2
MethodPISA
3
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6231
Polymers8,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
I: Ubiquitin thioesterase otubain-like
J: Ubiquitin aldehyde
K: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)58,0413
Polymers58,0413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-17 kcal/mol
Surface area22040 Å2
MethodPISA
5
L: Ubiquitin thioesterase otubain-like
M: Ubiquitin aldehyde
N: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)58,0413
Polymers58,0413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-19 kcal/mol
Surface area21810 Å2
MethodPISA
6
H: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6231
Polymers8,6231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.450, 182.815, 242.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4
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 aldehyde


Mass: 8560.831 Da / Num. of mol.: 4
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 /


Mass: 8622.922 Da / Num. of mol.: 2 / Mutation: G76C
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
#4: 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.: 4
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, 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-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 127533 / Num. obs: 127533 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.623 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23686 6451 5.1 %RANDOM
Rwork0.20277 ---
obs0.20448 120959 99.38 %-
all-127533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16069 0 0 309 16378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.97122300
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1952000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15124.473778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34152867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.45415105
X-RAY DIFFRACTIONr_chiral_restr0.0970.22497
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112449
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_it0.5391.510070
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.021216320
X-RAY DIFFRACTIONr_scbond_it1.55636363
X-RAY DIFFRACTIONr_scangle_it2.6974.55978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.347→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 441 -
Rwork0.319 7699 -
obs--92.14 %
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)
11.6514-0.26330.50380.3704-0.10932.95340.08180.03830.05240.02430.0318-0.1452-0.45790.2236-0.11360.2345-0.0792-0.01640.0579-0.03130.082-51.4466-51.8623102.461
27.1177-2.0312-2.22174.15990.15341.29410.19850.3083-0.206-0.0768-0.2180.240.3454-0.3130.01940.3358-0.1154-0.05690.2246-0.07170.0581-78.7456-47.132102.4928
32.3418-0.2064-1.14630.6372-0.18042.4499-0.04770.33660.31030.07330.0087-0.089-0.0004-0.27570.0390.260.0053-0.01850.13090.08230.1504-36.2109-47.270243.5612
46.3884-0.2649-1.18461.9641-0.00013.18860.06960.21910.8746-0.0183-0.0542-0.5292-0.34210.3954-0.01530.2507-0.0963-0.04380.14850.11820.4076-8.5344-44.47141.1423
56.57370.5882-2.80258.3514-5.56247.55980.7441-1.2366-0.91230.4125-0.06650.52690.6468-0.3609-0.67760.6754-0.5037-0.34380.58210.29680.3717-67.0069-74.685197.4812
61.41371.4709-0.45554.8694-1.10182.2987-0.0828-0.05560.0271-0.0190.21220.51170.0596-0.1728-0.12940.01790.0297-0.02030.12190.01340.1833-54.2903-71.1511131.887
71.4866-0.626-0.08762.57980.18451.0573-0.06080.0621-0.08140.0980.0763-0.15120.30010.1189-0.01550.2010.0261-0.01550.1462-0.07960.074-42.3688-107.0111135.0305
87.8674-0.2912-2.53551.91360.65813.086-0.10110.48510.0756-0.12140.12680.42680.2684-0.5424-0.02580.1414-0.0614-0.02290.26330.05120.2082-68.9327-99.5203138.5188
92.33160.23412.12072.62021.40833.8164-0.0384-0.1426-0.18220.0780.02360.17080.0385-0.23210.01470.2151-0.05380.09610.3128-0.20050.1903-49.7-133.736111.2366
101.69021.56390.11765.00942.40032.90440.19810.0060.13930.27170.1334-0.59350.29360.0565-0.33150.21210.0859-0.1040.0599-0.05250.546-39.0093-24.570271.8326
113.18160.32540.38442.67660.23551.1727-0.0194-0.1794-0.3562-0.0955-0.00350.06240.00910.19030.02290.00440.0066-0.00050.14340.04010.0477-7.5627-84.197248.2886
129.6059-1.51522.49462.1216-0.40762.64540.021-0.3215-0.4433-0.02230.06260.3267-0.0029-0.3402-0.08360.0042-0.0088-0.0280.12290.03850.2245-34.7887-83.856244.2305
131.889-2.0485-0.453213.98156.36774.0931.1583-0.52670.9952-0.2754-0.7367-1.3285-0.5471-0.7177-0.42161.2887-0.35780.54150.49680.04160.9881-28.8684-21.042135.0552
141.9787-0.7857-1.52472.39181.86545.0590.0220.2330.1796-0.0737-0.03150.177-0.3859-0.61930.00960.16050.0578-0.05630.28-0.00190.0713-4.5013-54.037671.2662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 275
2X-RAY DIFFRACTION2B501 - 576
3X-RAY DIFFRACTION3E31 - 275
4X-RAY DIFFRACTION4F501 - 576
5X-RAY DIFFRACTION5D501 - 571
6X-RAY DIFFRACTION6C3 - 151
7X-RAY DIFFRACTION7I36 - 276
8X-RAY DIFFRACTION8J501 - 576
9X-RAY DIFFRACTION9K3 - 150
10X-RAY DIFFRACTION10G3 - 150
11X-RAY DIFFRACTION11L38 - 275
12X-RAY DIFFRACTION12M501 - 576
13X-RAY DIFFRACTION13H501 - 571
14X-RAY DIFFRACTION14N2 - 151

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