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- PDB-5aaz: TBK1 recruitment to cytosol-invading Salmonella induces anti- bac... -

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Basic information

Entry
Database: PDB / ID: 5aaz
TitleTBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy
ComponentsOPTINEURIN
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling ...parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Golgi organization / autophagosome / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / trans-Golgi network / autophagy / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / Golgi membrane / innate immune response / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CNS
AuthorsThurston, T.l. / Allen, M.D. / Ravenhill, B. / Karpiyevitch, M. / Bloor, S. / Kaul, A. / Matthews, S. / Komander, D. / Holden, D. / Bycroft, M. / Randow, F.
CitationJournal: Embo J. / Year: 2016
Title: Recruitment of Tbk1 to Cytosol-Invading Salmonella Induces Wipi2-Dependent Antibacterial Autophagy.
Authors: Thurston, T.L. / Boyle, K.B. / Allen, M. / Ravenhill, B.J. / Karpiyevich, M. / Bloor, S. / Kaul, A. / Noad, J. / Foeglein, A. / Matthews, S.A. / Komander, D. / Bycroft, M. / Randow, F.
History
DepositionJul 31, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OPTINEURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5882
Polymers3,5221
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein/peptide OPTINEURIN / E3-14.7K-INTERACTING PROTEIN / FIP-2 / HUNTINGTIN YEAST PARTNER L / HUNTINGTIN-INTERACTING PROTEIN ...E3-14.7K-INTERACTING PROTEIN / FIP-2 / HUNTINGTIN YEAST PARTNER L / HUNTINGTIN-INTERACTING PROTEIN 7 / HIP-7 / HUNTINGTIN-INTERACTING PROTEIN L / NEMO-RELATED PROTEIN / OPTIC NEUROPATHY-INDUCING PROTEIN / TRANSCRIPTION FACTOR IIIA-INTERACTING PROTEIN / TFIIIA-INTP


Mass: 3522.147 Da / Num. of mol.: 1 / Fragment: RESIDES 548-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: HLTV PLASMID / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q96CV9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141HSQC
151HN(CA)CB
161CBCA(CO)NH
171HNCO
181HN(CA)CO
191HNHB
NMR detailsText: NONE

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 293.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIGstructure solution
CNSstructure solution
RefinementMethod: CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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