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Found 1 Document (1.216 seconds)

BMRB: 16284

2KIO

NMR structure of the oxidized yeast TOR1 FATC domain bound to DPC micelles at 318K

Authors

Dames, S.A.

Assembly

y1fatc

Entity

1. y1fatc (polymer, Thiol state: all disulfide bound), 33 monomers, 3960.446 Da Detail

NELDVPEQVD KLIQQATSIE RLCQHYIGWC PFW

Formula weight

3960.446 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS23:SG	1:CYS30:SG

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.5 %, Completeness (bb): 84.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.5 % (363 of 410)	92.5 % (198 of 214)	81.6 % (129 of 158)	94.7 % (36 of 38)
Backbone	84.0 % (163 of 194)	96.9 % (63 of 65)	72.4 % (71 of 98)	93.5 % (29 of 31)
Sidechain	93.5 % (232 of 248)	90.6 % (135 of 149)	97.8 % (90 of 92)	100.0 % (7 of 7)
Aromatic	91.3 % (42 of 46)	91.3 % (21 of 23)	90.5 % (19 of 21)	100.0 % (2 of 2)
Methyl	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)

1. y1fatc

NELDVPEQVD KLIQQATSIE RLCQHYIGWC PFW

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	y1fatc	[U-13C; U-15N]	0.40 mM
8	D2O	natural abundance	100 %
9	Tris	natural abundance	50 mM
10	NaCl	natural abundance	100 mM
11	dodecylphophocholine (DPC)	natural abundance	190-220 mM

Protein Blocks Logo

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

Release date

2010-12-01

Citation

Structural basis for the association of the redox-sensitive target of rapamycin FATC domain with membrane-mimetic micelles
Dames, S.A.
J. Biol. Chem. (2010), 285, 7766-7775, PubMed 20042596 , DOI 10.1074/jbc.M109.058404 , Abstract

Related entities 1. y1fatc, : 1 : 4 : 97 entities Detail

Interaction partners 1. y1fatc, : 71 interactors Detail

More details for 71 interactors identified by 11 citations

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

3 2D 1H-15N HSQC

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

4 2D 1H-13C HSQC

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

5 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

8 3D 1H-13C NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

9 3D 1H-13C NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	y1fatc	[U-13C; U-15N]	0.40 mM
8	D2O	natural abundance	100 %
9	Tris	natural abundance	50 mM
10	NaCl	natural abundance	100 mM
11	dodecylphophocholine (DPC)	natural abundance	190-220 mM

10 3D HNHB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

11 13C'-{13Cg} SED 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

12 15N-{13Cg} SED 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

13 {15N} SED 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

14 {13C'} SED 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

15 15N T1

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

16 15N T2

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

17 {1H}-15N-NOE

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	y1fatc	[U-13C; U-15N]	0.40-0.46 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	Tris	natural abundance	50 mM
5	NaCl	natural abundance	100 mM
6	dodecylphophocholine (DPC)	natural abundance	190-220 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16284_2kio.nef
Input source #2: Coordindates	2kio.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:23:CYS:SG	A:30:CYS:SG	oxidized, CA 60.813, CB 41.569 ppm	oxidized, CA 52.307, CB 44.287 ppm	2.021

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

--------10--------20--------30---
NELDVPEQVDKLIQQATSIERLCQHYIGWCPFW
|||||||||||||||||||||||||||||||||
NELDVPEQVDKLIQQATSIERLCQHYIGWCPFW

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	33	0	0	100.0

Content subtype: combined_16284_2kio.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assignments_y1fatc_dpc318	Warning	357		100.0 (chain: A, length: 33)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1578 (1)	noe	100.0 (chain: A, length: 33)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	61 (61)	.	97.0 (chain: A, length: 33)

Assigned chemical shifts

Saveframe: assignments_y1fatc_dpc318
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 198
  - ¹³C chemical shifts: 123
  - ¹⁵N chemical shifts: 36
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	214	198	92.5
¹³C chemical shifts	158	123	77.8
¹⁵N chemical shifts	39	36	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	63	96.9
¹³C chemical shifts	66	33	50.0
¹⁵N chemical shifts	31	29	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	135	90.6
¹³C chemical shifts	92	90	97.8
¹⁵N chemical shifts	8	7	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	21	91.3
¹³C chemical shifts	21	19	90.5
¹⁵N chemical shifts	2	2	100.0

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: 33, Sequence coverage: 100.0%
- Total number of restraints: 1475
- Weight of restraints: 1.0 (1475)
- Potential type of restraints: square-well-parabolic (1475)
- Range of distance target values: 2.3, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 97.0%
- Total number of restraints: 61
- Total number of restraints per polymer type: 61
- Weight of restraints: 1.0 (61)
- Potential type of restraints: square-well-parabolic (61)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords dodecylphospholine, FATC, lipid-binding motif, micelle, redox-state, target of rapamycin, TOR1, dpc micelle, membrane-mimetic, protein

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Found 1 Document (1.216 seconds)

BMRB: 16284

Sample #1

Sample #2

Related entities 1. y1fatc, : 1 : 4 : 97 entities Detail

Interaction partners 1. y1fatc, : 71 interactors Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 4 contents Detail