BMRB Entry 18464

Name: The solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger
Published: 2012-07-30

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PDB ID: 2lt9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18464
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

The solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger

Deposition date:

2012-05-15

Original release date:

2012-07-30

Authors:

Breukels, Vincent; Touw, Wouter; Vuister, Geerten

Citation:

Citation: Breukels, Vincent; Touw, Wouter; Vuister, Geerten. "NMR structure note: solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger" J. Biomol. NMR 54, 115-121 (2012).
PubMed: 22806131

Assembly members:

Assembly members:
NCX3, polymer, 157 residues, 16781.945 Da.

Natural source:

Natural source: Common Name: House mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET23b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
NCX3: MASHHHHHHHAGIFTFECDT IHVSESIGVMEVKVLRTSGA RGTVIVPFRTVEGTAKGGGE DFEDAYGELEFKNDETVKTI RVKIVDEEEYERQENFFIAL GEPKWMERGISEVTDRKLTV EEEEAKRIAEMGKPVLGEHP KLEVIIEESYEFKSTVD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	572
15N chemical shifts	135
1H chemical shifts	901

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	NCX3	1

Entities:

Entity 1, NCX3 157 residues - 16781.945 Da.

1

MET

ALA

SER

HIS

2

ALA

GLY

ILE

PHE

THR

PHE

GLU

CYS

ASP

THR

3

ILE

HIS

VAL

SER

GLU

SER

ILE

GLY

VAL

MET

4

GLU

VAL

LYS

VAL

LEU

ARG

THR

SER

GLY

ALA

5

ARG

GLY

THR

VAL

ILE

VAL

PRO

PHE

ARG

THR

6

VAL

GLU

GLY

THR

ALA

LYS

GLY

GLU

7

ASP

PHE

GLU

ASP

ALA

TYR

GLY

GLU

LEU

GLU

8

PHE

LYS

ASN

ASP

GLU

THR

VAL

LYS

THR

ILE

9

ARG

VAL

LYS

ILE

VAL

ASP

GLU

TYR

10

GLU

ARG

GLN

GLU

ASN

PHE

ILE

ALA

LEU

11

GLY

GLU

PRO

LYS

TRP

MET

GLU

ARG

GLY

ILE

12

SER

GLU

VAL

THR

ASP

ARG

LYS

LEU

THR

VAL

13

GLU

ALA

LYS

ARG

ILE

ALA

GLU

14

MET

GLY

LYS

PRO

VAL

LEU

GLY

GLU

HIS

PRO

15

LYS

LEU

GLU

VAL

ILE

GLU

SER

TYR

16

GLU

PHE

LYS

SER

THR

VAL

ASP

Samples:

sample_1: NCX3, [U-100% 13C; U-100% 15N], 0.5 ± 0.1 mM; HEPES 20 ± 0.1 mM; beta-mercaptoethanol 20 ± 0.1 mM; CaCl2 10 ± 0.1 mM; H2O 95 ± 0.1 %; D2O 5 ± 0.1 %

sample_pf1phage: NCX3, [U-100% 15N], 0.5 ± 0.1 mM; HEPES 20 ± 0.1 mM; beta-mercaptoethanol 20 ± 0.1 mM; CaCl2 10 ± 0.1 mM; Pf1 phage 8 ± 0.5 mg/mL; H2O 95 ± 0.1 %; D2O 5 ± 0.1 %

sample_isotrope: NCX3, [U-100% 15N], 0.5 ± 0.1 mM; HEPES 20 ± 0.1 mM; beta-mercaptoethanol 20 ± 0.1 mM; CaCl2 10 ± 0.1 mM; H2O 95 ± 0.1 %; D2O 5 ± 0.1 %

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 306 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_pf1phage	anisotropic	sample_conditions_1
2D 1H-13C IPAP HSQC	sample_isotrope	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

CCPN_Analysis v2.2.2, CCPN - chemical shift assignment, peak picking

NMRPipe v2007, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw v2007, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

YASARA v11.9.18, E. Krieger, Koraimann G, Vriend G - refinement

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 600 MHz

UNP	Q7TS90
PDB	2LT9
GB	EDL02702
AlphaFold	Q8VHJ8