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- PDB-5zq4: PDE-Ubi-ADPr -

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Basic information

Entry
Database: PDB / ID: 5zq4
TitlePDE-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 / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / 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 / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / 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 / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / 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 / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Deactivation of the beta-catenin transactivating complex / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of DVL / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / EGFR downregulation / Activation of NF-kappaB in B cells / Termination of translesion DNA synthesis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / Assembly Of The HIV Virion
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 MONOPHOSPHATE / Polyubiquitin-C / Uncharacterized protein laiD / SidE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.217 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
B: SidE
C: ubiquitin
A: SidE
D: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2936
Polymers104,5994
Non-polymers6942
Water2,126118
1
B: SidE
C: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6473
Polymers52,2992
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-12 kcal/mol
Surface area19610 Å2
MethodPISA
2
A: SidE
D: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6473
Polymers52,2992
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.417, 55.384, 98.435
Angle α, β, γ (deg.)90.00, 110.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SidE


Mass: 43578.441 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: 8720.961 Da / Num. of mol.: 2
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 10000, Bicine

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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: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 47640 / % possible obs: 99.4 % / Redundancy: 5.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Rrim(I) all: 0.102 / Net I/σ(I): 24.8
Reflection shellResolution: 2.23→2.27 Å / CC1/2: 0.886 / Rpim(I) all: 0.234 / Rrim(I) all: 0.587

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQ5

5zq5


Resolution: 2.217→48.428 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.45
RfactorNum. reflection% reflection
Rfree0.2258 2377 4.99 %
Rwork0.1809 --
obs0.1831 47640 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.217→48.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6829 0 46 118 6993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087021
X-RAY DIFFRACTIONf_angle_d1.1129484
X-RAY DIFFRACTIONf_dihedral_angle_d16.3972648
X-RAY DIFFRACTIONf_chiral_restr0.041013
X-RAY DIFFRACTIONf_plane_restr0.0061238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2168-2.2620.32281090.25932295X-RAY DIFFRACTION87
2.262-2.31120.30571380.23922669X-RAY DIFFRACTION98
2.3112-2.36490.29731670.2232615X-RAY DIFFRACTION100
2.3649-2.42410.29571430.21652647X-RAY DIFFRACTION100
2.4241-2.48960.28141360.21512666X-RAY DIFFRACTION100
2.4896-2.56290.25141620.20872657X-RAY DIFFRACTION99
2.5629-2.64560.25141520.20732691X-RAY DIFFRACTION100
2.6456-2.74010.25871410.20092667X-RAY DIFFRACTION100
2.7401-2.84980.25241270.21522657X-RAY DIFFRACTION99
2.8498-2.97950.29551330.21882722X-RAY DIFFRACTION100
2.9795-3.13660.24061390.21612657X-RAY DIFFRACTION99
3.1366-3.33310.21381340.19662713X-RAY DIFFRACTION100
3.3331-3.59030.2321390.1892686X-RAY DIFFRACTION100
3.5903-3.95150.23561400.17652712X-RAY DIFFRACTION99
3.9515-4.52290.19291330.15062711X-RAY DIFFRACTION100
4.5229-5.6970.20661450.1592719X-RAY DIFFRACTION99
5.697-48.43930.18481390.15332779X-RAY DIFFRACTION98
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)
14.26182.0743-0.01384.4859-0.08714.0261-0.49170.27040.4966-0.51850.4741-0.1239-0.63880.2443-0.00480.5828-0.0185-0.03970.2791-0.05230.429113.30593.3448-9.8774
22.5-0.4644-0.30473.6217-0.35912.6271-0.132-0.5190.150.48110.0071-0.2285-0.26070.08090.1280.4046-0.0045-0.07030.4045-0.01510.347614.265-3.28412.7631
32.9320.1447-0.39691.7054-0.41792.3761-0.0854-0.2973-0.41830.0795-0.2451-0.59610.4190.90980.18840.41050.10990.02130.55270.15740.536731.2939-17.7045-8.7681
44.6678-2.0741.21480.9776-0.92043.5873-0.03220.2341-0.3892-0.05-0.05120.06440.37890.20610.11830.4863-0.07180.02070.34990.00890.447719.4795-12.9771-19.0225
56.90370.8761-2.30623.43210.25965.2597-0.17131.13380.1538-0.26330.194-0.51990.2540.71210.11960.48820.05210.04290.86090.0920.526741.1399-12.9847-28.5063
69.31351.15593.15088.02290.26479.07660.33771.61710.953-0.67920.13870.2064-0.2650.1644-0.37820.4365-0.02630.05690.77820.24330.538236.7657-4.3399-31.1073
75.66361.4981-2.21376.32362.71926.0844-0.0195-0.1230.71870.6131-0.1218-0.6152-0.17161.57860.09260.5302-0.0343-0.02791.06310.18370.600943.3344-5.9486-22.3592
82.44390.12180.02484.33571.00163.4271-0.10860.53780.0619-0.3148-0.03780.3248-0.3221-0.23250.15570.470.0078-0.0110.5483-0.00020.34272.2146-5.3178-45.6725
91.9199-0.5583-0.4421.63381.0923.7523-0.03890.2953-0.38530.2924-0.49960.51430.718-1.21860.27570.4993-0.22020.11180.7246-0.24540.5636-12.3105-15.0778-31.547
109.8165-1.9856-1.19824.6931-0.94963.5658-0.7269-0.36830.00640.16220.16730.5590.1342-1.30170.51730.5464-0.17470.00191.2069-0.41070.6363-27.1091-5.7444-18.7244
118.07791.871.87786.22631.85478.05980.08420.65850.1047-0.0134-0.54660.8329-0.8169-0.90850.25360.48660.03880.01920.8729-0.26040.633-22.09283.2035-18.9814
125.62950.01870.6130.3170.36170.29880.01440.77660.2866-0.343-0.35060.7458-0.1098-0.95030.4140.6781-0.0671-0.02771.1004-0.27180.6782-27.2191-0.8834-26.7746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 222 through 275 )
2X-RAY DIFFRACTION2chain 'B' and (resid 276 through 393 )
3X-RAY DIFFRACTION3chain 'B' and (resid 394 through 513 )
4X-RAY DIFFRACTION4chain 'B' and (resid 514 through 576 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 22 )
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 44 )
7X-RAY DIFFRACTION7chain 'C' and (resid 45 through 73 )
8X-RAY DIFFRACTION8chain 'A' and (resid 222 through 393 )
9X-RAY DIFFRACTION9chain 'A' and (resid 394 through 576 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 22 )
11X-RAY DIFFRACTION11chain 'D' and (resid 23 through 44 )
12X-RAY DIFFRACTION12chain 'D' and (resid 45 through 74 )

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