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BMRB: 25602

2N2N

Tom1 negatively modulates binding of Tollip to phosphatidylinositol 3-phosphate via a coupled folding and binding mechanism

Authors

Xiao, S., Armstrong, G., Capelluto, D.

Assembly

GAT

Entity

1. GAT (polymer), 100 monomers, 11489.99 Da Detail

GPLGSEQIGK LRSELEMVSG NVRVMSEMLT ELVPTQAEPA DLELLQELNR TCRAMQQRVL ELIPQIANEQ LTEELLIVND NLNNVFLRHE RFERFRTGQT

Formula weight

11489.99 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

DISTANCE GEOMETRY, SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.0 %, Completeness: 39.0 %, Completeness (bb): 75.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	39.0 % (463 of 1186)	17.1 % (107 of 624)	59.4 % (268 of 451)	79.3 % (88 of 111)
Backbone	75.2 % (445 of 592)	46.3 % (93 of 201)	89.5 % (264 of 295)	91.7 % (88 of 96)
Sidechain	15.4 % (106 of 689)	3.8 % (16 of 423)	35.9 % (90 of 251)	0.0 % (0 of 15)
Aromatic	0.0 % (0 of 34)	0.0 % (0 of 17)	0.0 % (0 of 17)
Methyl	6.3 % (8 of 128)	4.7 % (3 of 64)	7.8 % (5 of 64)

1. entity

GPLGSEQIGK LRSELEMVSG NVRVMSEMLT ELVPTQAEPA DLELLQELNR TCRAMQQRVL ELIPQIANEQ LTEELLIVND NLNNVFLRHE RFERFRTGQT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2N2N, Strand ID: A Detail

Release date

2015-09-13

Citation

Tom1 Modulates Binding of Tollip to Phosphatidylinositol 3-Phosphate via a Coupled Folding and Binding Mechanism
Xiao, S., Brannon, M.K., Zhao, X., Fread, K.I., Ellena, J.F., Bushweller, J.H., Finkielstein, C.V., Armstrong, G.S., Capelluto, D.G.S.
Structure (2015), 23, 1910-1920, PubMed 26320582 , DOI 10.1016/j.str.2015.07.017 , Abstract

Related entities 1. GAT, : 1 : 2 : 2 : 46 entities Detail

Interaction partners 1. GAT, : 19 interactors Detail

More details for 19 interactors identified by 13 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

4 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

6 3D 1H- 15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

7 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Tom1 GAT	[U-99% 13C; U-99% 15N]		0.9 mM
2	Tollip TBD	natural abundance		1.1 mM
3	DSS	natural abundance		50 uM
4	potassium chloride	natural abundance		50 mM
5	TRIS	[U-2H]		20 mM
6	sodium azide	natural abundance		1 mM
7	DTT	[U-2H]		1 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_25602_2n2n.nef
Input source #2: Coordindates	2n2n.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

210-----220-------230-------240-------250-------260-------270-------280-------290-------300---------
GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTGQT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTGQT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	100	0	0	100.0

Content subtype: combined_25602_2n2n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	437		92.0 (chain: A, length: 100)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	164 (164)	.	89.0 (chain: A, length: 100)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 100, Sequence coverage: 92.0%
- Total number of assignments
  - ¹H chemical shifts: 87
  - ¹³C chemical shifts: 263
  - ¹⁵N chemical shifts: 87
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 100, Sequence coverage: 89.0%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein