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- PDB-4ddi: Crystal structure of human OTUB1/UbcH5b~Ub/Ub -

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Basic information

Entry
Database: PDB / ID: 4ddi
TitleCrystal structure of human OTUB1/UbcH5b~Ub/Ub
Components
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
KeywordsHYDROLASE/LIGASE / HYDROLASE-LIGASE complex / inhibition
Function / homology
Function and homology information


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-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 / Degradation of GLI1 by the proteasome
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.802 Å
AuthorsJuang, Y.C. / Sanches, M. / Sicheri, F.
CitationJournal: Mol.Cell / Year: 2012
Title: OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function.
Authors: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / ...Authors: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / Klevit, R.E. / Sicheri, F. / Durocher, D.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)188,8099
Polymers188,8099
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21610 Å2
ΔGint-80 kcal/mol
Surface area68440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.739, 106.225, 134.689
Angle α, β, γ (deg.)90.00, 123.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21E
31F
12A
22B
32C
13A
23B
33C
14G
24H
34I

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'D'D1 - 76
211chain 'E'E1 - 76
311chain 'F'F1 - 76
112chain 'A' and (resseq 1:150 ) and (not element H) and (not element D)A0
212chain 'B' and (resseq 1:150 ) and (not element H) and (not element D)B0
312chain 'C' and (resseq 1:150 ) and (not element H) and (not element D)C0
113chain 'A' and (resseq 1025:1271 ) and (not element H) and (not element D)A0
213chain 'B' and (resseq 1025:1271 ) and (not element H) and (not element D)B0
313chain 'C' and (resseq 1025:1271 ) and (not element H) and (not element D)C0
114chain 'G'G1 - 76
214chain 'H'H1 - 76
314chain 'I'I1 - 76

NCS ensembles :
ID
1
2
3
4
DetailsThere are three biological complexes per asymmetric unit. The biological complex defined by the author consists of Complex 1: chain H, chain E, residues 1 to 147 of chain C, and residues 1025-1071 of chain B; Complex 2: chain G, chain D, residues 1 to 147 of chain B, and residues 1025-1271 of chain a; Complex 3: chain I, chain F, residues 1 to 147 of chain A, and residues 1025-1271 of chain C;

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 / 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 / Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / Otubain-1 / hOTU1 / Ubiquitin-specific-processing protease OTUB1


Mass: 45782.543 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: UBE2D2, UBC4, UBC5B, UBCH4, UBCH5B, HSPC263, OTB1, OTU1, OTUB1
Production host: Escherichia coli (E. coli)
References: UniProt: P62837, UniProt: Q96FW1, ubiquitin-protein ligase, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-C / Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 6
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 25% PEG1500, 0.1 M SPG, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2011
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3.7958→49.47 Å / Num. all: 20217 / Num. obs: 19737 / % possible obs: 96.99 %
Reflection shellResolution: 3.7958→4.02 Å / % possible all: 83.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.802→49.469 Å / SU ML: 0.53 / σ(F): 1.99 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 986 5 %
Rwork0.2185 --
obs0.2212 19712 97.56 %
all-19745 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 155.341 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.7706 Å2-0 Å213.5838 Å2
2--9.2198 Å20 Å2
3----31.9904 Å2
Refinement stepCycle: LAST / Resolution: 3.802→49.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13284 0 0 0 13284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413563
X-RAY DIFFRACTIONf_angle_d1.02818330
X-RAY DIFFRACTIONf_dihedral_angle_d17.9715163
X-RAY DIFFRACTIONf_chiral_restr0.0812016
X-RAY DIFFRACTIONf_plane_restr0.0052391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D601X-RAY DIFFRACTIONPOSITIONAL0.002
12E601X-RAY DIFFRACTIONPOSITIONAL0.002
13F601X-RAY DIFFRACTIONPOSITIONAL0.002
21A1191X-RAY DIFFRACTIONPOSITIONAL0.002
22B1191X-RAY DIFFRACTIONPOSITIONAL0.002
23C1191X-RAY DIFFRACTIONPOSITIONAL0.002
31A2026X-RAY DIFFRACTIONPOSITIONAL0.001
32B2026X-RAY DIFFRACTIONPOSITIONAL0.001
33C2026X-RAY DIFFRACTIONPOSITIONAL0.002
41G601X-RAY DIFFRACTIONPOSITIONAL0.001
42H601X-RAY DIFFRACTIONPOSITIONAL0.001
43I601X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.802-4.00240.39271200.34022291X-RAY DIFFRACTION85
4.0024-4.25310.3411440.2962733X-RAY DIFFRACTION100
4.2531-4.58120.34551430.25882712X-RAY DIFFRACTION100
4.5812-5.04180.31991440.2252731X-RAY DIFFRACTION100
5.0418-5.77040.29081440.21582733X-RAY DIFFRACTION100
5.7704-7.26650.25011450.20892764X-RAY DIFFRACTION100
7.2665-49.47320.19651460.16782762X-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)
13.95720.09731.08455.46130.85583.74430.2830.24530.2765-0.18910.0553-0.1587-0.7772-0.003-0.26520.92850.16020.0490.59740.3220.557221.0875-11.000870.1738
24.07220.0137-0.61532.6677-1.2383.9602-0.46290.13340.3119-0.34650.0789-0.05870.91690.21660.01480.2020.1573-0.25580.41660.16970.3859.87454.038632.087
34.2007-0.532-1.13235.2664-1.87162.4180.0883-0.2668-0.35720.34550.11990.46110.5766-0.8756-0.16971.25610.2137-0.14581.63720.26070.8437-6.1634-13.656758.2366
42.32960.13231.24932.08360.3713.2235-0.17150.71351.5038-0.2393-0.30831.02470.0542-0.2737-0.0430.65540.36930.13531.00140.70152.3935-32.226710.66284.1217
54.12751.4326-0.16784.9311-0.78073.38070.0481-0.81780.3728-0.1515-0.24230.0526-0.07640.05780.17380.5834-0.07890.01520.415-0.15990.878215.008344.181624.563
62.21270.17150.52610.5687-0.97511.99650.52560.12571.15530.63810.15340.3063-1.8781-0.8409-0.35521.85870.72740.68531.10260.35971.2795-22.27466.752720.5718
73.39040.5012-0.40623.27251.76342.175-0.34182.023-1.8667-1.07530.20450.03751.2997-0.8008-0.20152.2664-0.3024-0.12991.9648-0.37481.19779.0514-16.852114.8154
82.67070.52350.36763.1051-1.65112.80741.2881-0.75251.16011.134-0.90341.6223-0.214-0.571-0.47221.4062-0.34530.49511.5643-0.1361.4817-47.3351-6.917498.5143
93.43611.37530.28933.48570.10511.9305-0.03961.0061-0.28940.02620.34130.21990.039-0.7573-0.2360.89540.62060.32421.72740.41830.8722-40.419648.915610.7962
103.0570.15360.50612.9482-1.5825.1388-0.5859-0.4676-0.5233-0.9925-0.1986-0.48421.96110.87020.62321.08990.32220.08230.76940.22180.620425.6837-15.004239.6103
113.91791.1877-1.81164.4405-0.62832.6192-0.0361-1.45830.02570.2598-0.7359-0.03260.1164-0.74340.70941.43-0.21180.05061.97-0.47031.694747.819241.579440.6735
125.0990.94811.26244.2773-0.76654.42690.6993-0.9880.43920.40520.2720.1898-0.70490.4136-0.66710.40020.04370.1041.0255-0.29950.719223.6009-5.2315105.5792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:150)
2X-RAY DIFFRACTION2chain 'A' and (resseq 1025:1271)
3X-RAY DIFFRACTION3chain 'B' and (resseq -1:150)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1025:1271)
5X-RAY DIFFRACTION5chain 'C' and (resseq -1:150)
6X-RAY DIFFRACTION6chain 'C' and (resseq 1025:1271)
7X-RAY DIFFRACTION7chain 'D' and (resseq 1:76)
8X-RAY DIFFRACTION8chain 'E' and (resseq 1:76)
9X-RAY DIFFRACTION9chain 'F' and (resseq 1:76)
10X-RAY DIFFRACTION10chain 'G' and (resseq 1:76)
11X-RAY DIFFRACTION11chain 'H' and (resseq 1:76)
12X-RAY DIFFRACTION12chain 'I' and (resseq 1:76)

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