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BMRB: 18958

2M3E

The Integrin L Transmembrane Domain in Bicelles: Structure and Interaction with Integrin 2

Authors

Surya, W., Li, Y., Millet, O., Diercks, T., Torres, J.

Assembly

Integrin L Transmembrane Domain

Entity

1. integrin aL TM domain (polymer, Thiol state: not present), 50 monomers, 5711.862 Da Detail

SNADVVYEKQ MLYLYVLSGI GGLLLLLLIF IVLYKVGFFK RNLKEKMEAG

2. PL (non-polymer, Thiol state: not present), na Da
3. (2S)-2-amino-3-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}butan-1-one (non-polymer, Thiol state: not present), 334.436 × 10 Da
4. 4-[(E)-(4-hydroxynaphthalen-1-yl)diazenyl]benzenesulfonic acid (non-polymer), 328.342 × 2 Da

Total weight

9712.905 Da

Max. entity weight

5711.862 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 84.5 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.5 % (534 of 632)	95.1 % (310 of 326)	68.4 % (173 of 253)	96.2 % (51 of 53)
Backbone	80.7 % (242 of 300)	96.2 % (101 of 105)	64.1 % (93 of 145)	96.0 % (48 of 50)
Sidechain	85.9 % (324 of 377)	91.9 % (203 of 221)	77.1 % (118 of 153)	100.0 % (3 of 3)
Aromatic	72.6 % (45 of 62)	93.5 % (29 of 31)	51.6 % (16 of 31)
Methyl	85.0 % (68 of 80)	95.0 % (38 of 40)	75.0 % (30 of 40)

1. integrin aL TM domain

SNADVVYEKQ MLYLYVLSGI GGLLLLLLIF IVLYKVGFFK RNLKEKMEAG

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M3E, Strand ID: A Detail

Release date

2014-01-26

Citation

Transmembrane and Juxtamembrane Structure of αL Integrin in Bicelles
Surya, W., Li, Y., Millet, O., Diercks, T., Torres, J.
PLoS One (2013), 8, e74281-e74281, PubMed 24069290 , DOI 10.1371/journal.pone.0074281 , Abstract

Related entities 1. integrin aL TM domain, : 1 : 2 : 15 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

2 3D HNCO

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

3 3D HNCA

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 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	integrin_aL_TM_domain	[U-100% 13C; U-100% 15N]		0.6 mM
2	potassium phosphate	natural abundance		50 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18958_2m3e.nef
Input source #2: Coordindates	2m3e.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

---1060------1070------1080------1090------1100---
SNADVVYEKQMLYLYVLSGIGGLLLLLLIFIVLYKVGFFKRNLKEKMEAG
||||||||||||||||||||||||||||||||||||||||||||||||||
SNADVVYEKQMLYLYVLSGIGGLLLLLLIFIVLYKVGFFKRNLKEKMEAG
--------10--------20--------30--------40--------50

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	50	0	0	100.0

Content subtype: combined_18958_2m3e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	548		100.0 (chain: A, length: 50)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	890 (1)	noe	98.0 (chain: A, length: 50)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 324
  - ¹³C chemical shifts: 170
  - ¹⁵N chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 98.0%
- Total number of restraints: 877
- Weight of restraints: 1.0 (877)
- Potential type of restraints: upper-bound-parabolic (877)
- Range of distance target values: 2.3, 5.5 (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

Keywords integrin aL TM domain