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- PDB-5yij: Structure of a Legionella effector with substrates -

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Basic information

Entry
Database: PDB / ID: 5yij
TitleStructure of a Legionella effector with substrates
Components
  • SdeA
  • Ubiquitin
KeywordsTRANSFERASE/PROTEIN BINDING / transferase / complex / alpha-helical domain / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / 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 ...NAD+-protein-arginine ADP-ribosyltransferase activity / 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 / protein deubiquitination / 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 / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / 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 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / positive regulation of protein ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Polyubiquitin-B / SdeA
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsFeng, Y. / Mu, Y. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670766 China
CitationJournal: Nature / Year: 2018
Title: Structural basis of ubiquitin modification by the Legionella effector SdeA.
Authors: Dong, Y. / Mu, Y. / Xie, Y. / Zhang, Y. / Han, Y. / Zhou, Y. / Wang, W. / Liu, Z. / Wu, M. / Wang, H. / Pan, M. / Xu, N. / Xu, C.Q. / Yang, M. / Fan, S. / Deng, H. / Tan, T. / Liu, X. / Liu, ...Authors: Dong, Y. / Mu, Y. / Xie, Y. / Zhang, Y. / Han, Y. / Zhou, Y. / Wang, W. / Liu, Z. / Wu, M. / Wang, H. / Pan, M. / Xu, N. / Xu, C.Q. / Yang, M. / Fan, S. / Deng, H. / Tan, T. / Liu, X. / Liu, L. / Li, J. / Wang, J. / Fang, X. / Feng, Y.
History
DepositionOct 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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: SdeA
C: Ubiquitin
D: Ubiquitin
G: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8605
Polymers136,1944
Non-polymers6651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-23 kcal/mol
Surface area56580 Å2
Unit cell
Length a, b, c (Å)107.779, 145.851, 103.349
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SdeA


Mass: 109787.945 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 236-1195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR0
#2: Protein Ubiquitin


Mass: 8802.056 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 1000, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 24125 / % possible obs: 99.7 % / Redundancy: 6.5 % / Net I/σ(I): 25.9
Reflection shellResolution: 3.18→3.31 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 5YIM

1ubq

5yim


Resolution: 3.18→39.956 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 1257 5.14 %
Rwork0.2261 --
obs0.2287 24116 92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→39.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9383 0 44 0 9427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049566
X-RAY DIFFRACTIONf_angle_d0.76312913
X-RAY DIFFRACTIONf_dihedral_angle_d14.6013655
X-RAY DIFFRACTIONf_chiral_restr0.0291455
X-RAY DIFFRACTIONf_plane_restr0.0051685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1803-3.30760.3535880.27431612X-RAY DIFFRACTION30
3.3076-3.45810.34321220.27312199X-RAY DIFFRACTION40
3.4581-3.64030.35621410.24322593X-RAY DIFFRACTION48
3.6403-3.86820.29531520.23652735X-RAY DIFFRACTION51
3.8682-4.16650.26861320.22152759X-RAY DIFFRACTION51
4.1665-4.58530.25821430.212751X-RAY DIFFRACTION51
4.5853-5.24750.26661480.21562765X-RAY DIFFRACTION51
5.2475-6.60650.3261730.25612821X-RAY DIFFRACTION53
6.6065-39.95880.18711580.19092944X-RAY DIFFRACTION54

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