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BMRB: 19041

2M59

Spatial structure of dimeric VEGFR2 membrane domain in DPC micelles

Authors

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

Assembly

VEGFR2tm

Entity

1. VEGFR2tm (polymer, Thiol state: not present), 37 monomers, 4127.031 × 2 Da Detail

EKTNLEIIIL VGTAVIAMFF WLLLVIILRT VKRANGG

Total weight

8254.062 Da

Max. entity weight

4127.031 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.7 %, Completeness (bb): 97.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.7 % (440 of 455)	100.0 % (231 of 231)	91.8 % (169 of 184)	100.0 % (40 of 40)
Backbone	97.3 % (216 of 222)	100.0 % (77 of 77)	94.4 % (102 of 108)	100.0 % (37 of 37)
Sidechain	96.3 % (257 of 267)	100.0 % (154 of 154)	90.9 % (100 of 110)	100.0 % (3 of 3)
Aromatic	71.9 % (23 of 32)	100.0 % (16 of 16)	40.0 % (6 of 15)	100.0 % (1 of 1)
Methyl	100.0 % (76 of 76)	100.0 % (38 of 38)	100.0 % (38 of 38)

1. VEGFR2tm

EKTNLEIIIL VGTAVIAMFF WLLLVIILRT VKRANGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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: 2M59, Strand ID: A, B Detail

Release date

2014-03-09

Related entities 1. VEGFR2tm, : 1 : 2 : 1 : 2 : 18 entities Detail

Interaction partners 1. VEGFR2tm, : 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR2tm	natural abundance		0.6 mM
2	VEGFR2tm	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		48 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 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19041_2m59.nef
Input source #2: Coordindates	2m59.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-------
EKTNLEIIILVGTAVIAMFFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILVGTAVIAMFFWLLLVIILRTVKRANGG

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

-------110-------120-------130-------
EKTNLEIIILVGTAVIAMFFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILVGTAVIAMFFWLLLVIILRTVKRANGG
--------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_19041_2m59.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	443		100.0 (chain: A, length: 37)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	710 (1)	noe	100.0 (chain: A, length: 37), 100.0 (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%
- Total number of assignments
  - ¹H chemical shifts: 232
  - ¹³C chemical shifts: 169
  - ¹⁵N chemical shifts: 42
- 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: 37, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 37, Sequence coverage: 100.0%
- Total number of restraints: 710
- Weight of restraints: 1.0 (710)
- Potential type of restraints: upper-bound-parabolic (710)
- 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

Keywords dimer, homodimer, receptor tyrosine kinase, VEGFR2