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

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Basic information

Entry
Database: PDB / ID: 5aaq
TitleTBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy
ComponentsCALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
KeywordsCALCIUM-BINDING PROTEIN / TBK1 / NDP52 / ZINC-FINGER
Function / homology
Function and homology information


xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle ...xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile.
Similarity search - Domain/homology
Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
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 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model
Revision 2.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8662
Polymers6,8011
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 CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2 / ANTIGEN NUCLEAR DOT 52 KDA PROTEIN / NUCLEAR DOMAIN 10 PROTEIN NDP52 / NUCLEAR DOMAIN 10 PROTEIN 52 ...ANTIGEN NUCLEAR DOT 52 KDA PROTEIN / NUCLEAR DOMAIN 10 PROTEIN NDP52 / NUCLEAR DOMAIN 10 PROTEIN 52 / NDP52 ZINC FINGER


Mass: 6800.896 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 388-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: HLTV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q13137
#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: 100 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 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
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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