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BMRB: 19941

2MOF

Structural insights of TM domain of LAMP-2A in DPC micelles

Authors

Tjandra, N., Rout, A., S, M., P, G.

Assembly

TM domain of LAMP-2A

Entity

1. TM domain of LAMP-2A (polymer, Thiol state: not present), 42 monomers, 4480.124 Da Detail

SADDDNFLVP IAVGAALAGV LILVLLAYFI GLKHHHAGYE QF

Formula weight

4480.124 Da

Source organism

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 78.4 %, Completeness (bb): 90.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.4 % (373 of 476)	73.8 % (175 of 237)	81.6 % (160 of 196)	88.4 % (38 of 43)
Backbone	90.0 % (225 of 250)	89.7 % (78 of 87)	89.3 % (109 of 122)	92.7 % (38 of 41)
Sidechain	68.9 % (182 of 264)	64.7 % (97 of 150)	75.9 % (85 of 112)	0.0 % (0 of 2)
Aromatic	43.1 % (25 of 58)	41.4 % (12 of 29)	44.8 % (13 of 29)
Methyl	82.9 % (58 of 70)	82.9 % (29 of 35)	82.9 % (29 of 35)

1. TM domain of LAMP2A

SADDDNFLVP IAVGAALAGV LILVLLAYFI GLKHHHAGYE QF

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
1	TM domain of LAMP2A	[U-99% 15N]		0.6 (±0.1) mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
4	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
7	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
8	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2014-10-26

Citation

Structure of transmembrane domain of lysosome-associated membrane protein type 2a (LAMP-2A) reveals key features for substrate specificity in chaperone-mediated autophagy
Tjandra, N., Rout, A., S, M., P, G.
J. Biol. Chem. (2014), 289, 35111-35123, PubMed 25342746 , DOI 10.1074/jbc.M114.609446 , Abstract

Related entities 1. TM domain of LAMP-2A, : 1 : 3 : 20 entities Detail

Interaction partners 1. TM domain of LAMP-2A, : 15 interactors Detail

More details for 15 interactors identified by 14 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
1	TM domain of LAMP2A	[U-99% 15N]		0.6 (±0.1) mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
4	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
4	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
4	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
4	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
4	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
1	TM domain of LAMP2A	[U-99% 15N]		0.6 (±0.1) mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 4D HCCH NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
7	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
8	D2O	natural abundance		100 %

9 3D 13C Filter NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.3, Details (15N/13C) TM-LAMP2A

#	Name	Isotope labeling	Type	Concentration
7	TM domain of LAMP2A	[U-99% 13C; U-99% 15N]		0.6 (±0.1) mM
8	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19941_2mof.nef
Input source #2: Coordindates	2mof.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

-370-----380-------390-------400-------410
SADDDNFLVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF
||||||||||||||||||||||||||||||||||||||||||
SADDDNFLVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF
--------10--------20--------30--------40--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	42	0	0	100.0

Content subtype: combined_19941_2mof.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	381		97.6 (chain: A, length: 42)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	409 (1)	noe	97.6 (chain: A, length: 42)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	34 (1)	hbond	50.0 (chain: A, length: 42)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	58 (58)	.	78.6 (chain: A, length: 42)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 97.6%
- Total number of assignments
  - ¹³C chemical shifts: 159
  - ¹H chemical shifts: 185
  - ¹⁵N chemical shifts: 37
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 97.6%
- Total number of restraints: 404
- Weight of restraints: 1.0 (404)
- Potential type of restraints: square-well-parabolic (404)
- Range of distance target values: 2.3, 4.8 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 50.0%
  - Total number of restraints: 34
  - Weight of restraints: 1.0 (34)
  - Potential type of restraints: square-well-parabolic (34)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 78.6%
- Total number of restraints: 58
- Total number of restraints per polymer type: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Protein