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BMRB: 19532

2MEU

NMR spatial structure of mutant dimeric TM domain of VEGFR2 receptor

Authors

Mineev, K.S., Arseniev, A.S., Lyukmanova, E.N., Shulepko, M.A., Kirpichnikov, M.P.

Assembly

mutant dimeric TM domain of VEGFR2 receptor

Entity

1. mutant dimeric TM domain of VEGFR2 receptor (polymer, Thiol state: not present), 37 monomers, 4181.033 × 2 Da Detail

EKTNLEIIIL VETAVIAMEF WLLLVIILRT VKRANGG

Total weight

8362.066 Da

Max. entity weight

4181.033 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.9 %, Completeness (bb): 99.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.9 % (448 of 453)	99.1 % (229 of 231)	98.4 % (179 of 182)	100.0 % (40 of 40)
Backbone	99.5 % (221 of 222)	100.0 % (76 of 76)	99.1 % (108 of 109)	100.0 % (37 of 37)
Sidechain	98.5 % (262 of 266)	98.7 % (153 of 155)	98.1 % (106 of 108)	100.0 % (3 of 3)
Aromatic	90.9 % (20 of 22)	100.0 % (11 of 11)	80.0 % (8 of 10)	100.0 % (1 of 1)
Methyl	100.0 % (76 of 76)	100.0 % (38 of 38)	100.0 % (38 of 38)

1. v2e 707

EKTNLEIIIL VETAVIAMEF WLLLVIILRT VKRANGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2013-10-06

Related entities 1. mutant dimeric TM domain of VEGFR2 receptor, : 1 : 4 : 19 entities Detail

Interaction partners 1. mutant dimeric TM domain of VEGFR2 receptor, : 30 interactors Detail

More details for 30 interactors identified by 19 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 13C,15N - filtered NOESY-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	v2e_707	natural abundance		0.6 mM
2	v2e_707	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19532_2meu.nef
Input source #2: Coordindates	2meu.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-------
EKTNLEIIILVETAVIAMEFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILVETAVIAMEFWLLLVIILRTVKRANGG

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

-------110-------120-------130-------
EKTNLEIIILVETAVIAMEFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILVETAVIAMEFWLLLVIILRTVKRANGG
--------10--------20--------30-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	37	0	0	100.0
B	B	37	0	0	100.0

Content subtype: combined_19532_2meu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	462		100.0 (chain: A, length: 37)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	566 (1)	noe	100.0 (chain: A, length: 37), 100.0 (chain: B, length: 37)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	1492 (1492)	.	97.3 (chain: A, length: 37), 97.3 (chain: B, length: 37)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%

--------10--------20--------30-------
EKTNLEIIILVETAVIAMEFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILVETAVIAMEFWLLLVIILRTVKRANGG

Total number of assignments
- ¹H chemical shifts: 236
- ¹³C chemical shifts: 182
- ¹⁵N chemical shifts: 44

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	THR	HG1	4.558
4	ASN	CG	175.448
13	THR	HG1	4.558
19	GLU	CD	129.753
29	ARG	HH21	6.901
29	ARG	HH22	6.901
29	ARG	NH2	72.508
30	THR	HG1	4.558
33	ARG	HH21	6.79
33	ARG	HH22	6.79
33	ARG	NH2	72.343
35	ASN	CG	176.485

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	231	228	98.7
¹³C chemical shifts	182	179	98.4
¹⁵N chemical shifts	42	42	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	75	98.7
¹³C chemical shifts	74	73	98.6
¹⁵N chemical shifts	37	37	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	153	98.7
¹³C chemical shifts	108	106	98.1
¹⁵N chemical shifts	5	5	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	39	100.0
¹³C chemical shifts	39	39	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	10	8	80.0
¹⁵N chemical shifts	1	1	100.0

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_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 37, Sequence coverage: 100.0%
- Total number of restraints: 566
- Weight of restraints: 1.0 (566)
- Potential type of restraints: upper-bound-parabolic (566)
- Range of distance target values: 0.0, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 97.3%
  - Entity_assembly_ID: B, Chain length: 37, Sequence coverage: 97.3%
- Total number of restraints: 1492
- Total number of restraints per polymer type: 1492
- Weight of restraints: 1.0 (1492)
- Potential type of restraints: square-well-parabolic (1492)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords VEGFR2, dimer, homodimer, receptor tyrosine kinase