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- PDB-5zq7: SidE-Ubi-NAD -

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Basic information

Entry
Database: PDB / ID: 5zq7
TitleSidE-Ubi-NAD
Components
  • SidE
  • Ubiquitin
KeywordsCELL INVASION / ubiquitination
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / 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 ...NAD+-protein-arginine ADP-ribosyltransferase activity / 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 / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / 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 / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / 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 / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
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 / Ubiquitin family ...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 MONOPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Polyubiquitin-C / Septation initiation protein / SidE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.847 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

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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)213,0328
Polymers211,0104
Non-polymers2,0214
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-64 kcal/mol
Surface area79130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.409, 129.381, 192.381
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 2.78 Å3/Da / Density % sol: 55.68 %
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: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 55129 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.05 / Rrim(I) all: 0.181 / Net I/σ(I): 13.2
Reflection shellResolution: 2.85→2.9 Å / CC1/2: 0.826 / Rpim(I) all: 0.305

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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: 2.847→48.939 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2394 2839 5.15 %
Rwork0.192 --
obs0.1944 55129 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.847→48.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14374 0 134 0 14508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714742
X-RAY DIFFRACTIONf_angle_d1.23719929
X-RAY DIFFRACTIONf_dihedral_angle_d10.4089077
X-RAY DIFFRACTIONf_chiral_restr0.0732217
X-RAY DIFFRACTIONf_plane_restr0.0092598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.847-2.89610.37661580.30192442X-RAY DIFFRACTION96
2.8961-2.94880.37111340.26782613X-RAY DIFFRACTION100
2.9488-3.00550.32741190.25462619X-RAY DIFFRACTION100
3.0055-3.06680.27121270.24732573X-RAY DIFFRACTION100
3.0668-3.13350.28691460.23212608X-RAY DIFFRACTION100
3.1335-3.20640.30671410.23892597X-RAY DIFFRACTION100
3.2064-3.28650.29861440.23962577X-RAY DIFFRACTION100
3.2865-3.37540.27671370.2292588X-RAY DIFFRACTION100
3.3754-3.47470.27431530.20882619X-RAY DIFFRACTION100
3.4747-3.58680.26591250.19422615X-RAY DIFFRACTION100
3.5868-3.71490.26771550.19322592X-RAY DIFFRACTION100
3.7149-3.86360.24081340.18712615X-RAY DIFFRACTION100
3.8636-4.03940.22511370.17292634X-RAY DIFFRACTION100
4.0394-4.25220.22111660.16022595X-RAY DIFFRACTION100
4.2522-4.51850.22521310.1532619X-RAY DIFFRACTION100
4.5185-4.86710.16291230.14842673X-RAY DIFFRACTION100
4.8671-5.35630.19121550.16282635X-RAY DIFFRACTION100
5.3563-6.13010.23171450.19112676X-RAY DIFFRACTION100
6.1301-7.71840.24261530.20012675X-RAY DIFFRACTION100
7.7184-48.94670.1951560.18232725X-RAY DIFFRACTION97
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)
11.81790.30950.19411.74820.91331.6320.133-0.22540.27090.0433-0.0496-0.1556-0.0190.0272-0.01430.2384-0.02720.0480.2798-0.03810.343978.217499.8758127.6828
21.12641.00190.10461.8213-0.72991.55380.2833-0.4223-0.24370.69-0.3091-0.22970.0716-0.0315-0.04190.5569-0.1898-0.06580.47020.02390.342273.618279.4568142.0069
30.72630.15630.31890.63940.5952.38590.08930.03370.0081-0.0277-0.07480.01860.1437-0.2933-0.01210.2353-0.0018-0.00190.2370.00540.265962.164176.655692.2371
41.82560.46610.1061.76890.05462.4458-0.2782-0.07370.03350.11430.0176-0.01280.4641-0.1884-0.10430.5551-0.1317-0.04190.47850.03970.476646.905315.34357.3957
50.51670.793-0.68232.5048-0.58251.7312-0.2271-0.18230.48830.3946-0.2394-0.2956-0.16770.45640.15640.63310.0283-0.00150.41650.11840.526272.2377107.089781.9845
63.4881-1.0292-0.64321.704-0.21961.51910.11750.5810.6864-0.7133-0.29260.1039-0.43230.55250.0470.4695-0.0038-0.02850.4750.16510.613870.5004101.394973.1909
71.05530.27321.17212.4239-0.17924.5385-0.01340.3612-0.0904-0.5630.00790.48820.20380.01520.00380.66690.1840.01860.51560.02150.573360.385198.417377.18
80.78770.91560.48541.85890.57151.4751-0.120.21190.53760.0728-0.0763-0.0052-0.2511-0.2740.00210.42530.00160.02220.3524-0.00740.439965.6172100.039280.1534
90.87470.3749-0.44920.1664-0.27391.34740.0435-0.41290.31850.1952-0.39530.802-0.1069-0.42810.15310.80420.05370.26271.52640.06821.2008-22.93942.211863.5005
102.79582.16040.33513.4169-0.1991.6164-0.2928-0.3929-0.40760.322-0.0060.73530.0988-1.07140.37830.632-0.35890.1621.2846-0.12761.3726-20.1892-3.445863.1832
116.2586-1.9768-1.67331.12990.64660.53390.1045-0.26160.10350.23050.1282-0.0438-0.0037-0.02050.05841.09160.19310.12352.1181-0.31311.4219-21.89889.850273.1708
127.44491.18460.61511.6816-1.9322.8022-0.1784-0.0626-0.49740.208-0.3005-0.05430.1232-0.06410.0290.8668-0.0210.35151.44250.16151.161-16.8482-0.591773.1383
130.05090.05060.0010.0504-0.00030.00250.2854-0.6014-0.72420.27240.16750.52420.4423-0.4494-0.18760.98530.10080.23761.45090.24211.116-9.7921-0.269369.1543
140.458-0.76071.09671.5394-1.5773.31550.2417-0.80110.27620.5295-0.1481-0.2303-0.10460.27230.11180.82950.1573-0.01981.735-0.28341.0506-11.939111.603366.0004
153.19024.6351.09058.12140.90250.71050.0377-0.16970.43620.1627-0.2406-0.0903-0.3650.38840.16451.67040.52610.42321.8138-0.10341.3838-18.04314.798469.1273
160.74710.95140.46321.22770.65940.94470.32860.15890.26410.3633-0.17850.8389-0.0879-0.9960.08080.64780.22510.1721.52590.31640.9003-13.97074.260663.6286
171.3631-0.03820.45121.7285-0.31092.00510.08440.177-0.2677-0.0551-0.06370.61070.3251-0.52520.07190.3161-0.0966-0.08690.4446-0.06960.6333-15.7381-10.200719.0592
181.48350.87610.32490.84640.03371.4877-0.12410.5894-0.4201-0.51930.29350.35220.165-0.15760.11430.3183-0.0846-0.15030.4333-0.09150.4413-8.834-4.411611.2619
191.07560.05540.68811.04530.12311.23690.02440.5181-0.2619-0.3070.1051-0.02640.30410.4083-0.03660.4265-0.03130.0070.508-0.10340.42938.5888-5.078815.4293
201.5879-0.12710.45711.5355-0.23681.8932-0.3675-0.28060.21760.53090.2025-0.091-0.5207-0.20850.01350.51130.1933-0.10030.3436-0.03660.309610.753514.791165.8864
211.4968-0.49450.31431.24610.06762.6292-0.1717-0.1098-0.12860.07660.13040.0907-0.1767-0.26730.02470.26340.0326-0.0160.26270.04940.29140.76286.460442.5198
221.47191.69011.82431.55922.10272.43750.2581-0.12510.12510.13620.0462-0.1462-0.3555-0.23310.12440.811-0.2889-0.07860.4567-0.11040.614342.038833.070974.7358
230.9878-0.08390.42561.24650.33551.0393-0.05210.27250.20990.601-0.23460.03830.25630.6135-0.09960.9718-0.3857-0.01770.82560.06360.676163.818137.598688.1886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 413 )
2X-RAY DIFFRACTION2chain 'A' and (resid 414 through 552 )
3X-RAY DIFFRACTION3chain 'A' and (resid 553 through 919 )
4X-RAY DIFFRACTION4chain 'A' and (resid 920 through 1058 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 44 )
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 76 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 7 )
10X-RAY DIFFRACTION10chain 'D' and (resid 8 through 16 )
11X-RAY DIFFRACTION11chain 'D' and (resid 17 through 23 )
12X-RAY DIFFRACTION12chain 'D' and (resid 24 through 34 )
13X-RAY DIFFRACTION13chain 'D' and (resid 35 through 44 )
14X-RAY DIFFRACTION14chain 'D' and (resid 45 through 54 )
15X-RAY DIFFRACTION15chain 'D' and (resid 55 through 59 )
16X-RAY DIFFRACTION16chain 'D' and (resid 60 through 76 )
17X-RAY DIFFRACTION17chain 'C' and (resid 223 through 372 )
18X-RAY DIFFRACTION18chain 'C' and (resid 373 through 447 )
19X-RAY DIFFRACTION19chain 'C' and (resid 448 through 612 )
20X-RAY DIFFRACTION20chain 'C' and (resid 613 through 750 )
21X-RAY DIFFRACTION21chain 'C' and (resid 751 through 894 )
22X-RAY DIFFRACTION22chain 'C' and (resid 895 through 950 )
23X-RAY DIFFRACTION23chain 'C' and (resid 951 through 1058 )

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