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BMRB: 17930

2LJD

monophosphorylated (747pY) beta3 integrin cytoplasmic tail under membrane mimetic conditions

Authors

Deshmukh, L., Vinogradova, O.

Assembly

monophosphorylated (747pY) beta3 integrin

Entity

1. monophosphorylated (747pY) beta3 integrin (polymer, Thiol state: not present), 67 monomers, 7819.471 Da Detail

GSSHHHHHHS SGLVPRGSHM KLLITIHDRK EFAKFEEERA RAKWDTANNP LXKEATSTFT NITYRGT

Formula weight

7819.471 Da

Source organism

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 73.1 %, Completeness: 72.2 %, Completeness (bb): 72.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.2 % (553 of 766)	72.6 % (289 of 398)	71.0 % (213 of 300)	75.0 % (51 of 68)
Backbone	72.4 % (284 of 392)	72.4 % (97 of 134)	72.2 % (140 of 194)	73.4 % (47 of 64)
Sidechain	72.5 % (316 of 436)	72.7 % (192 of 264)	71.4 % (120 of 168)	100.0 % (4 of 4)
Aromatic	53.7 % (44 of 82)	53.7 % (22 of 41)	52.5 % (21 of 40)	100.0 % (1 of 1)
Methyl	83.9 % (47 of 56)	85.7 % (24 of 28)	82.1 % (23 of 28)

1. entity

GSSHHHHHHS SGLVPRGSHM KLLITIHDRK EFAKFEEERA RAKWDTANNP LXKEATSTFT NITYRGT

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.11 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2LJD, Strand ID: A Detail

Release date

2011-10-19

Citation

Tyrosine phosphorylation as a conformational switch: a case study of integrin β3 cytoplasmic tail
Deshmukh, L., Meller, N., Alder, N., Byzova, T., Vinogradova, O.
J. Biol. Chem. (2011), 286, 40943-40953, PubMed 21956114 , DOI 10.1074/jbc.M111.231951 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 17931 released on 2011-10-19
    Title biphosphorylated (747pY, 759pY) beta3 integrin cytoplasmic tail under membrane mimetic conditions
  BMRB: 17932 released on 2011-10-19
    Title monophosphorylated (747pY) beta3 integrin cytoplasmic tail under aqueous conditions

Related entities 1. monophosphorylated (747pY) beta3 integrin, : 1 : 1 : 2 : 7 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.4 mM
2	DPC	[U-100% 2H]		150.0 ~ 300.0 mM
3	DSS	natural abundance		1 mM
4	sodium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17930_2ljd.nef
Input source #2: Coordindates	2ljd.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:51:LEU:C	1:52:PTR:N	unknown	unknown	n/a
1:52:PTR:C	1:53:LYS:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	747	PTR	O-PHOSPHOTYROSINE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--700-------710-------720-------730-------740-------750-------760--
GSSHHHHHHSSGLVPRGSHMKLLITIHDRKEFAKFEEERARAKWDTANNPLXKEATSTFTNITYRGT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSSHHHHHHSSGLVPRGSHMKLLITIHDRKEFAKFEEERARAKWDTANNPLXKEATSTFTNITYRGT
--------10--------20--------30--------40--------50--------60-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	67	0	0	100.0

Content subtype: combined_17930_2ljd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	545		70.1 (chain: A, length: 67)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	934 (1)	noe	70.1 (chain: A, length: 67)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	56 (56)	.	52.2 (chain: A, length: 67)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 70.1%
- Total number of assignments
  - ¹H chemical shifts: 283
  - ¹³C chemical shifts: 212
  - ¹⁵N chemical shifts: 50
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 70.1%
- Total number of restraints: 933
- Weight of restraints: 1.0 (933)
- Potential type of restraints: square-well-parabolic (933)
- Range of distance target values: 2.17, 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: 67, Sequence coverage: 52.2%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cell adhesion, integrin, tyrosine phosphorylation