BMRB Entry 15728

Name: NMR structures of dimeric transmembrane domain of the receptor tyrosine kinase EphA1 in lipid bicelles at pH 4.3
Published: 2008-09-02

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PDB ID: 2k1k
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15728
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2008-04-15

Original release date:

2008-09-02

Authors:

Mayzel, Maxim; Bocharov, Eduard; Arseniev, Alexander; Goncharuk, Marina

Citation:

Citation: Bocharov, Eduard; Mayzel, Maxim; Volynsky, Pavel; Goncharuk, Marina; Ermolyuk, Yaroslav; Schulga, Alexey; Artemenko, Elena; Efremov, Roman; Arseniev, Alexander. "Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1" J. Biol. Chem. 283, 29385-29395 (2008).
PubMed: 18728013

Assembly members:

Assembly members:
EphA1_TM, polymer, 38 residues, 3890.7 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PGEMEX1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
EphA1_TM: SPPVSRGLTGGEIVAVIFGL LLGAALLLGILVFRSRRA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts
coupling_constants
- hnha
- hnhb
heteronucl_NOEs
- heteronuclear_NOE
heteronucl_T1_relaxation
- T1_relax
heteronucl_T2_relaxation
- T2_relax

Data type	Count
13C chemical shifts	152
15N chemical shifts	35
1H chemical shifts	276
coupling constants	56
heteronuclear NOE values	30
T1 relaxation values	35
T2 relaxation values	34

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	EphA1 TM chain A	1
2	EphA1 TM chain B	1

Entities:

Entity 1, EphA1 TM chain A 38 residues - 3890.7 Da.

1

SER

PRO

VAL

SER

ARG

GLY

LEU

THR

GLY

2

GLY

GLU

ILE

VAL

ALA

VAL

ILE

PHE

GLY

LEU

3

LEU

GLY

ALA

LEU

GLY

ILE

4

LEU

VAL

PHE

ARG

SER

ARG

ALA

Samples:

EphA1_TM_15N_13C_homodimer: EphA1_TM 15N,13C, [U-15N; U-13C], 3 mM; DHPC, 2H, 96 mM; DMPC, 2H, 24 mM; NaN3 1.5 mkM; EDTA 1 mM; phosphate buffer 10 mM; D2O 100%

EphA1_TM_15N_homodimer: EphA1_TM 15N, [U-15N; U-13C], 3 mM; DHPC, 2H, 96 mM; DMPC, 2H, 24 mM; NaN3 1.5 mkM; EDTA 1 mM; phosphate buffer 10 mM; D2O 5%; H2O 95%

EphA1_TM_15N_13C_heterodimer: EphA1_TM 15N,13C, [U-15N; U-13C], 1.5 mM; DHPC, 2H, 96 mM; DMPC, 2H, 24 mM; NaN3 1.5 mkM; EDTA 1 mM; phosphate buffer 10 mM; EphA1_TM 1.5 mM; D2O 100%

pH_4.3: pH: 4.3; temperature: 313 K

pH_6.3: pH: 6.3; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	EphA1_TM_15N_homodimer	isotropic	pH_4.3
2D 1H-13C HSQC	EphA1_TM_15N_13C_homodimer	isotropic	pH_4.3
3D HNCO	EphA1_TM_15N_13C_homodimer	isotropic	pH_4.3
3D HNCA	EphA1_TM_15N_13C_homodimer	isotropic	pH_4.3
3D HN(CO)CA	EphA1_TM_15N_13C_homodimer	isotropic	pH_4.3
3D HCCH-TOCSY	EphA1_TM_15N_13C_homodimer	isotropic	pH_4.3
3D HNHA	EphA1_TM_15N_homodimer	isotropic	pH_4.3
3D HNHB	EphA1_TM_15N_homodimer	isotropic	pH_4.3
3D 1H-15N NOESY	EphA1_TM_15N_homodimer	isotropic	pH_4.3
3D 1H-15N TOCSY	EphA1_TM_15N_homodimer	isotropic	pH_4.3
3D 1H-13C NOESY	EphA1_TM_15N_13C_homodimer	isotropic	pH_4.3
13C F1-filtered/F3-edited-NOESY	EphA1_TM_15N_13C_heterodimer	isotropic	pH_4.3
15N-T1	EphA1_TM_15N_homodimer	isotropic	pH_4.3
15N-T2	EphA1_TM_15N_homodimer	isotropic	pH_4.3
15N-NOE	EphA1_TM_15N_homodimer	isotropic	pH_4.3
2D 1H-15N HSQC	EphA1_TM_15N_homodimer	isotropic	pH_6.3

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CARA v1.5.5, 1.8, Keller and Wuthrich - chemical shift assignment

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Varian Unity 600 600 MHz MHz

PDB	2K1K 2K1L
DBJ	BAF83040
EMBL	CAA81796
GB	AAA36747 AAD43440 AAI30292 AAS07458 AIC54347
REF	NP_005223 XP_002751927 XP_003270912 XP_003791590 XP_003820582
SP	P21709
AlphaFold	P21709