BMRBj - BMREntryMaster

Found 1 Document (1.637 seconds)

BMRB: 25736

5AAY

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. NF-KAPPA-B ESSENTIAL MODULATOR (polymer, Thiol state: free and disulfide bound), 30 monomers, 3399.886 Da Detail

GSPPDFCCPK CQYQAPDMDT LQIHVMECIE

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

Total weight

3465.295 Da

Max. entity weight

3399.886 Da

Source organism

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 92.1 %, Completeness (bb): 93.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.1 % (313 of 340)	97.8 % (175 of 179)	86.4 % (114 of 132)	82.8 % (24 of 29)
Backbone	93.0 % (160 of 172)	94.7 % (54 of 57)	92.1 % (82 of 89)	92.3 % (24 of 26)
Sidechain	91.9 % (181 of 197)	99.2 % (121 of 122)	83.3 % (60 of 72)	0.0 % (0 of 3)
Aromatic	45.5 % (10 of 22)	90.9 % (10 of 11)	0.0 % (0 of 11)
Methyl	100.0 % (20 of 20)	100.0 % (10 of 10)	100.0 % (10 of 10)

1. NF-KAPPA-B ESSENTIAL MODULATOR

GSPPDFCCPK CQYQAPDMDT LQIHVMECIE

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 5AAY, 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

Related entities 1. NF-KAPPA-B ESSENTIAL MODULATOR, : 1 : 8 : 34 entities Detail

Interaction partners 1. NF-KAPPA-B ESSENTIAL MODULATOR, : 18 interactors Detail

More details for 18 interactors identified by 11 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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

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	NF-KAPPA-B ESSENTIAL MODULATOR	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25736_5aay.nef
Input source #2: Coordindates	5aay.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	1:8:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:11:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:24:HIS:NE2	unknown	unknown	n/a
2:1:ZN:ZN	1:28:CYS:SG	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

390-----400-------410---------
GSPPDFCCPKCQYQAPDMDTLQIHVMECIE
||||||||||||||||||||||||||||||
GSPPDFCCPKCQYQAPDMDTLQIHVMECIE
--------10--------20--------30

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	30	0	0	100.0

Content subtype: combined_25736_5aay.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	313		96.7 (chain: A, length: 30)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	778 (1)	noe	96.7 (chain: A, length: 30)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	undefined	13.3 (chain: A, length: 30)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	9 (9)	.	30.0 (chain: A, length: 30)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	36 (36)	.	83.3 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 175
  - ¹³C chemical shifts: 114
  - ¹⁵N chemical shifts: 24
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 96.7%
- Total number of restraints: 777
- Weight of restraints: 1.0 (777)
- Potential type of restraints: square-well-parabolic (777)
- 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: 30, Sequence coverage: 13.3%
  - 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: 30, Sequence coverage: 30.0%
- Total number of restraints: 9
- Total number of restraints per polymer type: 9
- Weight of restraints: 1.0 (9)
- Potential type of restraints: square-well-parabolic (9)
- 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: 30, Sequence coverage: 83.3%
  - Total number of restraints: 36
  - Total number of restraints per polymer type: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: square-well-parabolic (36)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords PROTEIN BINDING