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- PDB-7bu0: Crystal structure of a OTU deubiquitinase in complex with Ub-PA -

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Basic information

Entry
Database: PDB / ID: 7bu0
TitleCrystal structure of a OTU deubiquitinase in complex with Ub-PA
Components
  • Polyubiquitin-B
  • Uncharacterized protein
KeywordsHYDROLASE / complex
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / 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 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / SCF(Skp2)-mediated degradation of p27/p21
Similarity search - Function
: / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Ubiquitin B / Polyubiquitin-B / Dot/Icm T4SS effector
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å
AuthorsOuyang, S.Y. / Zhen, X.K.
CitationJournal: Elife / Year: 2020
Title: Interplay between bacterial deubiquitinase and ubiquitin E3 ligase regulates ubiquitin dynamics on Legionella phagosomes.
Authors: Liu, S. / Jiwei, L. / Zhen, X. / Qiu, J. / Ouyang, S. / Luo, Z.Q.
History
DepositionApr 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_validate_close_contact ...database_2 / pdbx_validate_close_contact / refine_ls_restr_ncs / reflns / struct_conn / struct_ncs_dom / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns.number_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Polyubiquitin-B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5776
Polymers114,4624
Non-polymers1142
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.930, 119.230, 84.530
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 48711.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSI8
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39, UniProt: P0CG47*PLUS
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Magnesium formate dihydrate 15% w/v PEG 3350 / PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.43→118.95 Å / Num. obs: 49112 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.994 / Net I/σ(I): 9.2
Reflection shellResolution: 2.43→2.52 Å / Num. unique obs: 3613 / CC1/2: 0.781 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.43→48.615 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.78
RfactorNum. reflection% reflection
Rfree0.2552 1990 4.05 %
Rwork0.2149 --
obs0.2166 49112 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.02 Å2 / Biso mean: 61.9874 Å2 / Biso min: 21.11 Å2
Refinement stepCycle: final / Resolution: 2.43→48.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7750 0 8 200 7958
Biso mean--23.13 56.38 -
Num. residues----964
LS refinement shellResolution: 2.43→2.4908 Å
RfactorNum. reflection
Rfree0.4235 136
Rwork0.375 -
obs-3289
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)
11.3807-0.53930.64961.0773-0.58762.0033-0.0563-0.10470.0766-0.1674-0.0760.19110.074-0.0651-0.06890.3952-0.0221-0.02490.3694-0.00220.4984-10.2390.771126.5955
22.7412-0.67460.97151.47260.41031.21440.0817-0.5915-0.64360.10070.03730.22940.1337-0.0081-0.00650.358-0.03020.09030.5360.18580.57551.8408-16.010946.7297
32.2588-0.4480.00621.614-0.86730.9986-0.03230.1469-0.0842-0.3731-0.14-0.1110.15370.078-0.04310.48130.02360.00390.36220.00270.4389-6.09670.017217.8591
42.00590.25090.48492.5091-0.4651.93230.1826-0.1678-0.099-0.3351-0.0370.26330.1931-0.226-0.17120.7044-0.0149-0.05880.54580.09220.616-23.87630.0388-4.0254
55.9218-1.1115-1.08564.002-0.35363.84460.04760.0411-0.15650.338-0.0542-0.12150.2539-0.35-0.06340.67330.0301-0.07060.51790.05040.5485-18.289532.62082.854
61.3923-0.69090.62451.6172-0.77430.9941-0.0709-0.2048-0.06-0.20980.0533-0.06680.22050.3220.0250.54490.06350.09810.40180.03260.586818.4831.63745.317
70.6752-0.2585-0.68411.6659-0.15752.65410.0558-0.05920.0694-0.2842-0.087-0.1923-0.12470.840.07910.5360.03120.09520.4930.08780.507621.50123.35942.906
84.92710.2423-5.24020.3734-0.29385.60750.089-0.7666-0.17890.0615-0.4067-0.8239-0.29681.22850.31330.3360.04760.02680.68230.21130.514814.19624.95531.907
94.99931.8606-0.27121.98470.45391.99620.3761-0.2205-0.36530.2918-0.1534-0.6012-0.03640.55210.11880.59230.06420.07460.62320.13120.77420.74229.21331.697
100.8547-0.6932-0.27472.0552-0.67141.0439-0.1679-0.4311-0.2862-0.1423-0.0773-0.54290.32320.06780.04060.51170.07670.04560.47270.09360.549211.99726.85540.696
110.7277-0.01910.27641.6271-0.98042.2611-0.0088-0.06210.0320.3504-0.10020.0784-0.17780.01540.03970.4652-0.02880.04740.4509-0.06480.43934.214822.633648.85
122.0024-0.0495-0.14472.6594-0.3261.8911-0.04690.36760.0088-0.13760.0230.0423-0.11570.09560.03470.5856-0.0528-0.06650.5892-0.0270.45715.5649-11.077583.1114
130.6865-0.16850.46030.20210.05860.72760.0976-0.3478-0.20110.4123-0.32090.0938-0.51550.15450.13730.4937-0.05760.02820.4286-0.09420.60792.392-15.28223.778
140.1850.1662-0.1490.8126-0.48650.5552-0.2197-0.0425-0.03090.2796-0.1051-0.3252-0.23520.25080.17070.5822-0.1536-0.02830.669-0.00170.64296.73-14.53622.111
151.1880.3390.54772.5881-0.91761.73570.13790.2873-0.40280.5146-0.1278-1.23550.03290.61080.20030.4813-0.0881-0.07720.65890.01480.583211.366-7.45519.084
160.01660.2552-0.00294.0954-0.0507-0.00080.010.21360.09240.0278-0.1727-0.316-0.02490.15340.07440.4582-0.05650.08010.6007-0.05180.37156.52-6.61630.892
172.61492.80581.03973.08030.99157.34730.12260.6004-0.2392-0.40950.0204-0.3436-0.18820.55920.0410.4184-0.05140.00460.6924-0.06440.500212.683-8.36834.794
182.31851.2523-2.06439.62741.1272.40.10690.0535-0.4393-0.25840.17260.04550.1179-0.04740.16350.4004-0.14240.00570.84230.04330.585316.828-13.42130.568
190.99760.5581-0.29961.3999-1.17391.2952-0.10990.0670.1138-0.06280.204-0.3257-0.2613-0.22920.1060.5046-0.014-0.01080.51-0.05380.48554.653-9.40330.229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 159 )A11 - 159
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 236 )A160 - 236
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 319 )A237 - 319
4X-RAY DIFFRACTION4chain 'A' and (resid 320 through 393 )A320 - 393
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 417 )A394 - 417
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 23 )D1 - 23
7X-RAY DIFFRACTION7chain 'D' and (resid 24 through 46 )D24 - 46
8X-RAY DIFFRACTION8chain 'D' and (resid 47 through 51 )D47 - 51
9X-RAY DIFFRACTION9chain 'D' and (resid 52 through 56 )D52 - 56
10X-RAY DIFFRACTION10chain 'D' and (resid 57 through 75 )D57 - 75
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 319 )B10 - 319
12X-RAY DIFFRACTION12chain 'B' and (resid 320 through 416 )B320 - 416
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 7 )C1 - 7
14X-RAY DIFFRACTION14chain 'C' and (resid 8 through 23 )C8 - 23
15X-RAY DIFFRACTION15chain 'C' and (resid 24 through 41 )C24 - 41
16X-RAY DIFFRACTION16chain 'C' and (resid 42 through 46 )C42 - 46
17X-RAY DIFFRACTION17chain 'C' and (resid 47 through 51 )C47 - 51
18X-RAY DIFFRACTION18chain 'C' and (resid 52 through 56 )C52 - 56
19X-RAY DIFFRACTION19chain 'C' and (resid 57 through 75 )C57 - 75

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