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Found 1 Document (0.872 seconds)

BMRB: 15728

2K1K

NMR structures of dimeric transmembrane domain of the receptor tyrosine kinase EphA1 in lipid bicelles at pH 4.3

Authors

Mayzel, M.L., Bocharov, E.V., Arseniev, A.S., Goncharuk, M.V.

Assembly

EphA1 TM dimer

Entity

1. EphA1 TM dimer (polymer, Thiol state: not present), 38 monomers, 3890.665 × 2 Da Detail

SPPVSRGLTG GEIVAVIFGL LLGAALLLGI LVFRSRRA

Total weight

7781.33 Da

Max. entity weight

3890.665 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, coupling_constants, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.6 %, Completeness (bb): 94.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (386 of 426)	91.7 % (199 of 217)	87.9 % (152 of 173)	97.2 % (35 of 36)
Backbone	94.2 % (211 of 224)	96.2 % (77 of 80)	91.7 % (99 of 108)	97.2 % (35 of 36)
Sidechain	88.5 % (207 of 234)	89.1 % (122 of 137)	87.6 % (85 of 97)
Aromatic	60.0 % (12 of 20)	100.0 % (10 of 10)	20.0 % (2 of 10)
Methyl	97.1 % (68 of 70)	94.3 % (33 of 35)	100.0 % (35 of 35)

1. EphA1 TM

SPPVSRGLTG GEIVAVIFGL LLGAALLLGI LVFRSRRA

Show sample condition

Sample #1

Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

Sample #2

Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

Sample #3

Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
16	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	1.5 mM
17	DHPC	2H	lipid	96 mM
18	DMPC	2H	lipid	24 mM
19	NaN3	natural abundance		1.5 uM
20	EDTA	natural abundance		1 mM
21	phosphate buffer	natural abundance	buffer	10 mM
22	EphA1_TM	natural abundance	protein	1.5 mM
23	D2O			100 %

Protein Blocks Logo

Calculated from 12 models in PDB: 2K1K, Strand ID: A, B Detail

Heteronucl. T₁

35 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600 MHz, Temperature 313 (±0.1) K, pH 4.3 (±0.1) Detail

Heteronucl. T₂

34 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Temperature 313 (±0.1) K, pH 4.3 (±0.1) Detail

Heteronucl. NOE

30 NOE values in 1 lists
Value type na, Field strength (¹H) 600 MHz, Temperature 313 (±0.1) K, pH 4.3 (±0.1) Detail

Heteronucl. T₁/T₂

34 T₁/T₂ values in 1 lists
Field strength (¹H) 600 MHz, Temperature 313 (±0.1) K, pH 4.3 (±0.1) Detail

Coupling constant

56 J values in 2 lists
Field strength (¹H) 600 MHz, Temperature 313 (±0.1) K, pH 4.3 (±0.1) Detail

Release date

2008-09-01

Citation

Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1
Bocharov, E.V., Mayzel, M.L., Volynsky, P.E., Goncharuk, M.V., Ermolyuk, Y.S., Schulga, A.A., Artemenko, E.O., Efremov, R.G., Arseniev, A.S.
J. Biol. Chem. (2008), 283, 29385-29395, PubMed 18728013 , DOI 10.1074/jbc.M803089200 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P21709 released on 1991-05-01
Title EPHA1_HUMAN Entity Ephrin type-A receptor 1

Related entities 1. EphA1 TM dimer, : 1 : 3 : 21 entities Detail

Interaction partners 1. EphA1 TM dimer, : 6 interactors Detail

More details for 6 interactors identified by 5 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

2 2D 1H-13C HSQC

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

3 3D HNCO

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

4 3D HNCA

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

5 3D HN(CO)CA

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

6 3D HCCH-TOCSY

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

7 3D HNHA

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

8 3D HNHB

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

9 3D 1H-15N NOESY

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

10 3D 1H-15N TOCSY

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

11 3D 1H-13C NOESY

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
1	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	3 mM
2	DHPC	2H	lipid	96 mM
3	DMPC	2H	lipid	24 mM
4	NaN3	natural abundance		1.5 uM
5	EDTA	natural abundance		1 mM
6	phosphate buffer	natural abundance	buffer	10 mM
7	D2O			100 %

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

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
16	EphA1_TM 15N,13C	[U-15N; U-13C]	protein	1.5 mM
17	DHPC	2H	lipid	96 mM
18	DMPC	2H	lipid	24 mM
19	NaN3	natural abundance		1.5 uM
20	EDTA	natural abundance		1 mM
21	phosphate buffer	natural abundance	buffer	10 mM
22	EphA1_TM	natural abundance	protein	1.5 mM
23	D2O			100 %

13 15N-T1

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

14 15N-T2

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

15 15N-NOE

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 4.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

16 2D 1H-15N HSQC

Instrument

Varian Unity 600 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 313 (±0.1) K, pH 6.3 (±0.1), Details peptide in DHPC/DMPC bicelles

#	Name	Isotope labeling	Type	Concentration
8	EphA1_TM 15N	[U-15N; U-13C]	protein	3 mM
9	DHPC	2H	lipid	96 mM
10	DMPC	2H	lipid	24 mM
11	NaN3	natural abundance		1.5 uM
12	EDTA	natural abundance		1 mM
13	phosphate buffer	natural abundance	buffer	10 mM
14	D2O			5 %
15	H2O	natural abundance		95 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15728_2k1k.nef
Input source #2: Coordindates	2k1k.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

--540-------550-------560-------570---
SPPVSRGLTGGEIVAVIFGLLLGAALLLGILVFRSRRA
||||||||||||||||||||||||||||||||||||||
SPPVSRGLTGGEIVAVIFGLLLGAALLLGILVFRSRRA
--------10--------20--------30--------

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

--540-------550-------560-------570---
SPPVSRGLTGGEIVAVIFGLLLGAALLLGILVFRSRRA
||||||||||||||||||||||||||||||||||||||
SPPVSRGLTGGEIVAVIFGLLLGAALLLGILVFRSRRA
--------10--------20--------30--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	38	0	0	100.0
B	B	38	0	0	100.0

Content subtype: combined_15728_2k1k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts	Warning	394		100.0 (chain: A, length: 38)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1426 (1)	noe	100.0 (chain: A, length: 38), 100.0 (chain: B, length: 38)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	56 (55)	.	78.9 (chain: A, length: 38)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 207
  - ¹³C chemical shifts: 152
  - ¹⁵N chemical shifts: 35
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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	217	206	94.9
¹³C chemical shifts	173	152	87.9
¹⁵N chemical shifts	40	35	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	79	98.8
¹³C chemical shifts	76	68	89.5
¹⁵N chemical shifts	36	35	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	127	92.7
¹³C chemical shifts	97	84	86.6
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	35	100.0
¹³C chemical shifts	35	35	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	2	20.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 38, Sequence coverage: 100.0%
- Total number of restraints: 1418
- Weight of restraints: 1.0 (1418)
- Potential type of restraints: upper-bound-parabolic (1418)
- Range of distance target values: 2.38, 6.24 (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_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 78.9%
- Total number of restraints: 55
- Total number of restraints per polymer type: 55
- Weight of restraints: 1.0 (55)
- Potential type of restraints: square-well-parabolic (55)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords dimeric transmembrane domen, EphA1, receptor tyrosine kinase

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Found 1 Document (0.872 seconds)

BMRB: 15728

Sample #1

Sample #2

Sample #3

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. EphA1 TM dimer, : 1 : 3 : 21 entities Detail

Interaction partners 1. EphA1 TM dimer, : 6 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail