BMRBj - BMREntryMaster

Found 1 Document (1.484 seconds)

BMRB: 16005

2K9Y

EphA2 dimeric structure in the lipidic bicelle at pH 5.0

Authors

Mayzel, M.L., Bocharov, E.V., Areniev, A.S.

Assembly

EphA2 TM dimer

Entity

1. EphA2 TM dimer (polymer, Thiol state: not present), 41 monomers, 4278.009 × 2 Da Detail

EFQTLSPEGS GNLAVIGGVA VGVVLLLVLA GVGFFIHRRR K

Total weight

8556.018 Da

Max. entity weight

4278.009 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

TORSION ANGLE DYNAMICS, molecular dynamics, TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.4 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.4 % (438 of 464)	94.5 % (223 of 236)	93.5 % (174 of 186)	97.6 % (41 of 42)
Backbone	97.5 % (238 of 244)	98.9 % (87 of 88)	96.6 % (112 of 116)	97.5 % (39 of 40)
Sidechain	92.1 % (234 of 254)	91.9 % (136 of 148)	92.3 % (96 of 104)	100.0 % (2 of 2)
Aromatic	58.8 % (20 of 34)	58.8 % (10 of 17)	58.8 % (10 of 17)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. EphA2 TM

EFQTLSPEGS GNLAVIGGVA VGVVLLLVLA GVGFFIHRRR K

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	3 mM
2	DHPC	[U-2H]	lipid	96 mM
3	DMPC	[U-2H]	lipid	24 mM
4	NaN3	natural abundance		1.5 mM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
13	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	1.5 mM
14	DHPC	[U-2H]	lipid	96 mM
15	DMPC	[U-2H]	lipid	24 mM
16	NaN3	natural abundance		1.5 mM
17	EDTA	natural abundance		1 mM
18	phosphate buffer	natural abundance	buffer	10 mM
19	EphA2_TM	natural abundance	protein	1.5 mM

Protein Blocks Logo

Calculated from 17 models in PDB: 2K9Y, Strand ID: A, B Detail

Release date

2010-05-05

Citation

Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases
Bocharov, E.V., Mayzel, M.L., Volynsky, P.E., Mineev, K.S., Tkach, E.N., Ermolyuk, Y.S., Schulga, A.A., Efremov, R.G., Arseniev, A.S.
Biophys. J. (2010), 98, 881-889, PubMed 20197042 , DOI 10.1016/j.bpj.2009.11.008 , Abstract

Related entities 1. EphA2 TM dimer, : 1 : 2 : 64 entities Detail

Interaction partners 1. EphA2 TM dimer, : 24 interactors Detail

More details for 24 interactors identified by 14 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

2 2D 1H-13C HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	3 mM
2	DHPC	[U-2H]	lipid	96 mM
3	DMPC	[U-2H]	lipid	24 mM
4	NaN3	natural abundance		1.5 mM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM

3 3D HNCO

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	3 mM
2	DHPC	[U-2H]	lipid	96 mM
3	DMPC	[U-2H]	lipid	24 mM
4	NaN3	natural abundance		1.5 mM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM

4 3D HNCA

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	3 mM
2	DHPC	[U-2H]	lipid	96 mM
3	DMPC	[U-2H]	lipid	24 mM
4	NaN3	natural abundance		1.5 mM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM

5 3D HCCH-TOCSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	3 mM
2	DHPC	[U-2H]	lipid	96 mM
3	DMPC	[U-2H]	lipid	24 mM
4	NaN3	natural abundance		1.5 mM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM

6 3D 1H-15N NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

7 3D 1H-15N TOCSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

8 3D 1H-13C NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	3 mM
2	DHPC	[U-2H]	lipid	96 mM
3	DMPC	[U-2H]	lipid	24 mM
4	NaN3	natural abundance		1.5 mM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM

9 3D HNHB

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

10 3D HNHA

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

11 2D 1H-1H NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

12 13C F1-filtered/F3-edited-NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
13	EphA2_TM	[U-95% 13C; U-95% 15N]	protein	1.5 mM
14	DHPC	[U-2H]	lipid	96 mM
15	DMPC	[U-2H]	lipid	24 mM
16	NaN3	natural abundance		1.5 mM
17	EDTA	natural abundance		1 mM
18	phosphate buffer	natural abundance	buffer	10 mM
19	EphA2_TM	natural abundance	protein	1.5 mM

13 15N-T2

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

14 15N-T1

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

15 15N-NOE

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

16 2D 1H-1H TOCSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
7	EphA2_TM	[U-95% 15N]	protein	3 mM
8	DHPC	[U-2H]	lipid	96 mM
9	DMPC	[U-2H]	lipid	24 mM
10	NaN3	natural abundance		1.5 mM
11	EDTA	natural abundance		1 mM
12	phosphate buffer	natural abundance	buffer	10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16005_2k9y.nef
Input source #2: Coordindates	2k9y.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

-----530-------540-------550-------560---
EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK
|||||||||||||||||||||||||||||||||||||||||
EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK
--------10--------20--------30--------40-

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

-----530-------540-------550-------560---
EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK
|||||||||||||||||||||||||||||||||||||||||
EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK
--------10--------20--------30--------40-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	41	0	0	100.0
B	B	41	0	0	100.0

Content subtype: combined_16005_2k9y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts	Warning	437		100.0 (chain: A, length: 41)
1	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	846 (1)	noe	97.6 (chain: A, length: 41), 97.6 (chain: B, length: 41)
2	Distance restraints	DYANA/DIANA_distance_constraints_7	OK	102 (1)	noe	36.6 (chain: A, length: 41), 36.6 (chain: B, length: 41)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	120 (1)	hbond	58.5 (chain: A, length: 41), 58.5 (chain: B, length: 41)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 222
  - ¹³C chemical shifts: 174
  - ¹⁵N chemical shifts: 41
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	236	222	94.1
¹³C chemical shifts	186	174	93.5
¹⁵N chemical shifts	45	41	91.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	87	98.9
¹³C chemical shifts	82	78	95.1
¹⁵N chemical shifts	40	39	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	148	135	91.2
¹³C chemical shifts	104	96	92.3
¹⁵N chemical shifts	5	2	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	34	100.0
¹³C chemical shifts	34	34	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	10	58.8
¹³C chemical shifts	17	10	58.8

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 97.6%
  - Entity_assembly_ID: B, Chain length: 41, Sequence coverage: 97.6%
- Total number of restraints: 846
- Weight of restraints: 1.0 (846)
- Potential type of restraints: upper-bound-parabolic (846)
- Range of distance target values: 2.37, 5.83 (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
- Saveframe: DYANA/DIANA_distance_constraints_7
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 36.6%
    - Entity_assembly_ID: B, Chain length: 41, Sequence coverage: 36.6%
  - Total number of restraints: 102
  - Weight of restraints: 1.0 (102)
  - Potential type of restraints: upper-bound-parabolic (102)
  - Range of distance target values: 3.0, 5.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 58.5%
      - Entity_assembly_ID: B, Chain length: 41, Sequence coverage: 58.5%
    - Total number of restraints: 120
    - Weight of restraints: 1.0 (120)
    - Potential type of restraints: upper-bound-parabolic (120)
    - Range of distance target values: 2.3, 3.5 (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 dimeric transmembrane domain, ephrin receptor, membrane protein, receptor tyrosine kinase

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Found 1 Document (1.484 seconds)

BMRB: 16005

Sample #1

Sample #2

Sample #3

Related entities 1. EphA2 TM dimer, : 1 : 2 : 64 entities Detail

Interaction partners 1. EphA2 TM dimer, : 24 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail