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BMRB: 25742

5AAZ

TBK1 recruitment to cytosol-invading Salmonella induces anti-bacterial autophagy

Authors

Thurston, T.L., Allen, M.D., Ravenhill, B., Karpiyevitch, M., Bloor, S., Kaul, A., Matthews, S., Komander, D., Holden, D., Bycroft, M., Randow, F., Matthews, A.

Assembly

TBK1 recruitment to cytosol-invading Salmonella induces anti-bacterial autophagy

Entity

1. OPTINEURIN (polymer, Thiol state: all disulfide bound), 32 monomers, 3518.113 Da Detail

GSRNIPIHSC PKCGEVLPDI DTLQIHVMDC II

2. ZINC ION (non-polymer), 65.409 Da

Total weight

3583.522 Da

Max. entity weight

3518.113 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS10:SG	1:CYS13:SG

Source organism

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 85.0 %, Completeness (bb): 90.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.0 % (306 of 360)	94.1 % (176 of 187)	73.9 % (105 of 142)	80.6 % (25 of 31)
Backbone	90.9 % (169 of 186)	92.1 % (58 of 63)	91.5 % (86 of 94)	86.2 % (25 of 29)
Sidechain	80.9 % (165 of 204)	95.2 % (118 of 124)	60.3 % (47 of 78)	0.0 % (0 of 2)
Aromatic	50.0 % (4 of 8)	100.0 % (4 of 4)	0.0 % (0 of 4)
Methyl	90.5 % (38 of 42)	95.2 % (20 of 21)	85.7 % (18 of 21)

1. OPTINEURIN

GSRNIPIHSC PKCGEVLPDI DTLQIHVMDC II

Show sample condition

Sample

Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5AAZ, Strand ID: A Detail

Release date

2016-07-10

Citation

Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy
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.
EMBO J. (2016), 35, 1779-1792, PubMed 27370208 , DOI 10.15252/embj.201694491 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 25734 released on 2016-07-10
    Title TBK1 recruitment to cytosol-invading Salmonella induces anti-bacterial autophagy
  BMRB: 25736 released on 2016-07-10
    Title TBK1 recruitment to cytosol-invading Salmonella induces anti-bacterial autophagy

Related entities 1. OPTINEURIN, : 1 : 5 : 32 entities Detail

Interaction partners 1. OPTINEURIN, : 60 interactors Detail

More details for 60 interactors identified by 19 citations

Experiments performed 9 experiments Detail

1 NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

2 TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

3 DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

4 HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

5 HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

6 CBCACONH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

7 HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

8 HNCACO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

9 HNHB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	OPTINEURIN	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Tris	natural abundance		10 mM
5	NaCl	natural abundance		135 mM
6	B-mercaptoethanol	natural abundance		5 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25742_5aaz.nef
Input source #2: Coordindates	5aaz.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:1:ZN:ZN	1:13:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:30:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:10:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:26:HIS:NE2	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-490-----500-------510-------520
GSRNIPIHSCPKCGEVLPDIDTLQIHVMDCII
||||||||||||||||||||||||||||||||
GSRNIPIHSCPKCGEVLPDIDTLQIHVMDCII
--------10--------20--------30--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	32	0	0	100.0

Content subtype: combined_25742_5aaz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	305		93.8 (chain: A, length: 32)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	730 (1)	noe	93.8 (chain: A, length: 32)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	undefined	12.5 (chain: A, length: 32)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	10 (10)	.	31.2 (chain: A, length: 32)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	46 (46)	.	90.6 (chain: A, length: 32)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 176
  - ¹³C chemical shifts: 104
  - ¹⁵N chemical shifts: 25
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 93.8%
- Total number of restraints: 726
- Weight of restraints: 1.0 (726)
- Potential type of restraints: square-well-parabolic (726)
- Range of distance target values: 2.3, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 12.5%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 3.45, 3.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 31.2%
- Total number of restraints: 10
- Total number of restraints per polymer type: 10
- Weight of restraints: 1.0 (10)
- Potential type of restraints: square-well-parabolic (10)
- Dihedral angle restraints per residue
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 90.6%
  - Total number of restraints: 46
  - Total number of restraints per polymer type: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords PROTEIN BINDING