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BMRB: 17424

2L8S

Solution NMR Structure of Transmembrane and Cytosolic Regions of Integrin 1 in Detergent Micelles

Authors

Lai, C., Liu, X., Tian, C.

Assembly

Integrin 1

Entity

1. Integrin 1 (polymer, Thiol state: all free), 54 monomers, 6329.810 Da Detail

MGLPGRVPLW VILLSAFAGL LLLMLLILAL WKIGFFKRPL KKKMEKLEHH HHHH

Formula weight

6329.81 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.5 %, Completeness: 59.2 %, Completeness (bb): 78.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.2 % (419 of 708)	52.0 % (192 of 369)	65.4 % (187 of 286)	75.5 % (40 of 53)
Backbone	78.0 % (248 of 318)	78.0 % (85 of 109)	78.5 % (124 of 158)	76.5 % (39 of 51)
Sidechain	47.7 % (210 of 440)	41.2 % (107 of 260)	57.3 % (102 of 178)	50.0 % (1 of 2)
Aromatic	15.4 % (12 of 78)	20.5 % (8 of 39)	8.1 % (3 of 37)	50.0 % (1 of 2)
Methyl	52.4 % (43 of 82)	46.3 % (19 of 41)	58.5 % (24 of 41)

1. Integrin Alpha1

MGLPGRVPLW VILLSAFAGL LLLMLLILAL WKIGFFKRPL KKKMEKLEHH HHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	DTT	natural abundance		2 mM
3	Integrin Alpha 1	[U-15N]		1.0 mM
4	H20	natural abundance		95 %
5	D20	natural abundance		5 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2L8S, Strand ID: A Detail

Release date

2012-08-13

Citation

Integrin α1 has a long helix, extending from the transmembrane region to the cytoplasmic tail in detergent micelles
Lai, C., Liu, X., Tian, C., Wu, F.
PLoS One (2013), 8, e62954-e62954, PubMed 23646163 , DOI 10.1371/journal.pone.0062954 , Abstract

Related entities 1. Integrin 1, : 1 : 6 : 28 entities Detail

Interaction partners 1. Integrin 1, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	DTT	natural abundance		2 mM
3	Integrin Alpha 1	[U-15N]		1.0 mM
4	H20	natural abundance		95 %
5	D20	natural abundance		5 %

2 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

3 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

4 3D HNCA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

7 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

8 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

9 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Integrin Alpha1	[U-13C; U-15N]		1.0 mM
7	sodium phosphate	natural abundance		50 mM
8	DTT	natural abundance		2 mM
9	H20	natural abundance		90 %
10	D20	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17424_2l8s.nef
Input source #2: Coordindates	2l8s.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

--------10--------20--------30--------40--------50----
MGLPGRVPLWVILLSAFAGLLLLMLLILALWKIGFFKRPLKKKMEKLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGLPGRVPLWVILLSAFAGLLLLMLLILALWKIGFFKRPLKKKMEKLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	54	0	0	100.0

Content subtype: combined_17424_2l8s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	384		79.6 (chain: A, length: 54)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	241 (1)	noe	55.6 (chain: A, length: 54)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	60 (60)	.	61.1 (chain: A, length: 54)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	32 (32)	.	59.3 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 79.6%
- Total number of assignments
  - ¹H chemical shifts: 170
  - ¹³C chemical shifts: 176
  - ¹⁵N chemical shifts: 38
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 55.6%
- Total number of restraints: 241
- Weight of restraints: 1.0 (241)
- Potential type of restraints: square-well-parabolic (241)
- Range of distance target values: 2.65, 4.15 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 61.1%
- Total number of restraints: 60
- Total number of restraints per polymer type: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 59.3%
- Total number of restraints: 32
- Potential type of restraints: undefined (32)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Detergent micelle, Integrin Alpha1, NMR Structure, Transmembrane Region