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- PDB-5zq6: SidE-Ubi-ADPr -

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Basic information

Entry
Database: PDB / ID: 5zq6
TitleSidE-Ubi-ADPr
Components
  • SidE
  • Ubiquitin
KeywordsCELL INVASION / ubiquitination
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / protein deubiquitination / 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 ...NAD+-protein-arginine ADP-ribosyltransferase activity / protein deubiquitination / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport / Hedgehog ligand biogenesis
Similarity search - Function
SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / : / 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
ADENOSINE-5'-DIPHOSPHATE / Polyubiquitin-C / Uncharacterized protein laiD / SidE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.009 Å
AuthorsWang, Y. / Gao, A. / Gao, P.
Funding support China, 4items
OrganizationGrant numberCountry
91753133 China
31670903 China
31700687 China
XDB08020204 China
CitationJournal: Cell / Year: 2018
Title: Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.
Authors: Wang, Y. / Shi, M. / Feng, H. / Zhu, Y. / Liu, S. / Gao, A. / Gao, P.
History
DepositionApr 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SidE
B: Ubiquitin
D: Ubiquitin
C: SidE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,8656
Polymers211,0104
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-59 kcal/mol
Surface area78680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.322, 128.003, 191.065
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 SidE


Mass: 96813.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR1, UniProt: Q6BBR6*PLUS
#2: Protein Ubiquitin


Mass: 8691.896 Da / Num. of mol.: 2 / Mutation: R42A
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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tacsimate

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 45143 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.07 / Rrim(I) all: 0.191 / Net I/σ(I): 12.6
Reflection shellResolution: 3.01→3.1 Å / CC1/2: 0.795 / Rpim(I) all: 0.399

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQ5

5zq5


Resolution: 3.009→20.943 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.31
RfactorNum. reflection% reflection
Rfree0.2316 2272 5.03 %
Rwork0.1801 --
obs0.1828 45143 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.009→20.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14341 0 54 0 14395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714704
X-RAY DIFFRACTIONf_angle_d0.98719873
X-RAY DIFFRACTIONf_dihedral_angle_d8.0628975
X-RAY DIFFRACTIONf_chiral_restr0.0482205
X-RAY DIFFRACTIONf_plane_restr0.0072594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0087-3.07390.36151370.27192366X-RAY DIFFRACTION88
3.0739-3.14520.31561470.24782629X-RAY DIFFRACTION100
3.1452-3.22360.37041460.2422673X-RAY DIFFRACTION100
3.2236-3.31040.25871490.22382667X-RAY DIFFRACTION100
3.3104-3.40740.25251270.22772664X-RAY DIFFRACTION100
3.4074-3.51690.31071440.22742674X-RAY DIFFRACTION100
3.5169-3.6420.27961470.2222658X-RAY DIFFRACTION99
3.642-3.7870.25611420.20052682X-RAY DIFFRACTION100
3.787-3.95820.26771410.20442676X-RAY DIFFRACTION100
3.9582-4.16540.21751350.15452704X-RAY DIFFRACTION100
4.1654-4.4240.21011160.14472730X-RAY DIFFRACTION100
4.424-4.76190.1621440.13752695X-RAY DIFFRACTION100
4.7619-5.23430.22881530.14012708X-RAY DIFFRACTION100
5.2343-5.97630.19851480.17022720X-RAY DIFFRACTION100
5.9763-7.47230.2131510.18272768X-RAY DIFFRACTION100
7.4723-20.94390.1791450.15412857X-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)
11.78080.30340.47972.69530.91495.4435-0.0902-0.3482-0.01760.3025-0.0135-0.0330.34540.05050.02710.6023-0.1228-0.04750.63870.02440.481351.022317.11961.4545
25.2708-0.96132.89695.8759-2.23016.1102-0.4951-0.16510.65460.00060.54320.7274-0.9599-0.2838-0.14650.73210.0159-0.02660.56110.10630.964169.2462106.514178.7065
33.1845-1.4925-2.10272.782-0.87623.04770.00610.95840.9957-0.80860.131-0.1426-1.31720.4552-0.05990.7624-0.0609-0.01140.78780.27750.936372.0575101.471871.9167
42.1309-1.51831.37666.7059-1.90845.2582-0.22440.4026-0.3227-0.8184-0.220.0078-0.08450.01610.32180.59210.00630.01220.54310.07550.590865.231296.214476.2293
53.5458-0.05590.42724.47971.5493.0433-0.23880.34010.77240.1113-0.07460.0666-0.6223-0.14320.33120.66070.00540.0690.48450.07230.526665.126699.12279.6385
64.9553.14570.11092.3415-1.21825.47480.0479-0.47150.36160.3472-0.42761.3778-0.7478-1.33590.27031.0410.26350.05121.2905-0.07681.1454-23.03282.121162.9265
78.74551.2757-1.84891.3459-1.75462.2758-0.2423-1.04570.11660.75770.17820.92150.3111-1.47310.19380.9567-0.12030.22191.4846-0.06481.1252-21.50891.550466.9058
85.54091.3995-0.86872.0242-3.15295.5862-0.0736-1.5104-0.31570.31180.00530.20720.4675-0.48730.14930.59530.12660.26511.85890.2361.3739-16.936-0.473672.6378
91.5343-0.9233-0.91139.6129-6.50266.3794-0.0012-0.9289-0.99080.85480.00130.62210.613-0.9358-0.02660.99140.20560.29031.41330.57351.1447-9.9221-0.285868.7021
103.7891-2.1799-2.15017.5772-1.88532.76980.0603-1.3290.471.2059-0.05030.4293-0.63090.0761-0.12761.29580.3582-0.12271.8158-0.44931.2013-13.004211.668966.5293
113.8573-2.0648-2.38462.7472-0.14352.71730.28990.2445-0.0026-0.18980.25980.3738-0.00970.2334-0.29380.81680.77520.24371.67480.10391.4674-22.498812.918964.295
122.0091.9689-0.67654.52491.61564.82090.42970.8024-0.22920.4822-0.22920.0738-0.4217-1.1817-0.21190.67680.11970.13380.94980.2310.6895-7.51740.402863.7612
132.1170.61560.73063.2868-0.45272.4761-0.0650.2693-0.3492-0.21920.17780.74280.3924-0.6739-0.06770.4246-0.1189-0.06190.6318-0.06240.7895-15.966-8.964217.1529
141.3391-0.18360.84771.1120.29972.8984-0.16760.01-0.09410.05720.17140.0474-0.1597-0.0058-0.00020.31320.00980.03360.29970.05210.41066.10614.558138.1017
151.93271.47321.90032.03361.62342.09310.07880.2650.2690.60320.0348-0.28420.07750.5249-0.07041.022-0.2581-0.06930.8646-0.01320.746255.774935.596982.9699
163.30420.57470.38042.49180.3422.19110.0876-0.15160.15060.1529-0.0465-0.2214-0.09880.0455-0.04550.2618-0.01050.04850.3038-0.02830.330377.449298.6907126.9368
172.13290.4275-0.1932.6819-1.37033.24260.174-0.5216-0.32660.7552-0.2253-0.13970.15140.01270.02820.5491-0.1718-0.09850.43960.03050.395772.778178.409141.1154
181.2590.22870.65560.93530.7663.4570.08640.02030.0483-0.1042-0.09510.10980.2322-0.4860.01310.2584-0.00180.01640.31620.02130.321761.569572.998885.4059
191.89760.1392-0.59122.2541-0.09374.81930.12170.05910.1415-0.0149-0.08670.01-0.3515-0.1079-0.02490.2490.0091-0.01350.2745-0.03570.303763.125183.2426101.1233
200.76133.79853.64787.67099.31439.65190.06370.0071-0.0738-0.42760.0922-0.1302-0.356-0.0363-0.1370.9966-0.2796-0.18030.8967-0.11880.694445.931736.887969.6304
214.22010.10110.79414.76170.3612.1264-0.2607-0.1267-0.376-0.3511-0.2023-0.18350.88850.0060.5080.9695-0.2350.10390.52680.12670.697942.82766.127451.2193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 989 through 1058 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 22 )
3X-RAY DIFFRACTION3chain 'B' and (resid 23 through 34 )
4X-RAY DIFFRACTION4chain 'B' and (resid 35 through 56 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 76 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 7 )
7X-RAY DIFFRACTION7chain 'D' and (resid 8 through 22 )
8X-RAY DIFFRACTION8chain 'D' and (resid 23 through 34 )
9X-RAY DIFFRACTION9chain 'D' and (resid 35 through 44 )
10X-RAY DIFFRACTION10chain 'D' and (resid 45 through 56 )
11X-RAY DIFFRACTION11chain 'D' and (resid 57 through 65 )
12X-RAY DIFFRACTION12chain 'D' and (resid 66 through 76 )
13X-RAY DIFFRACTION13chain 'C' and (resid 223 through 413 )
14X-RAY DIFFRACTION14chain 'C' and (resid 414 through 894 )
15X-RAY DIFFRACTION15chain 'C' and (resid 895 through 1058 )
16X-RAY DIFFRACTION16chain 'A' and (resid 222 through 413 )
17X-RAY DIFFRACTION17chain 'A' and (resid 414 through 552 )
18X-RAY DIFFRACTION18chain 'A' and (resid 553 through 750 )
19X-RAY DIFFRACTION19chain 'A' and (resid 751 through 894 )
20X-RAY DIFFRACTION20chain 'A' and (resid 895 through 949 )
21X-RAY DIFFRACTION21chain 'A' and (resid 950 through 988 )

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