BMRB Entry 19050

Name: Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2
Published: 2014-07-21

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PDB ID: 2m5e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19050
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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:

Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2

Deposition date:

2013-02-21

Original release date:

2014-07-21

Authors:

Fowler, C.; Feldkamp, Michael; Yu, Liping; Shea, Madeline

Citation:

Citation: Hovey, Liam; Fowler, C; Mahling, Ryan; Lin, Zesen; Miller, Mark; Marx, Dagan; Yoder, Jesse; Kim, Elaine; Tefft, Kristin; Waite, Brett; Feldkamp, Michael; Yu, Liping; Shea, Madeline. "Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel NaV1.2." Biophys. Chem. 224, 1-19 (2017).
PubMed: 28343066

Assembly members:

Assembly members:
C-domain_of_Calmodulin_(residues_76-148), polymer, 73 residues, 8416.369 Da.
IQ_motif_peptide_of_NaV1-2_(residues_1901-1927), polymer, 27 residues, 3370.125 Da.
CALCIUM ION, non-polymer, 40.078 Da.

Natural source:

Natural source: Common Name: Ciliates Taxonomy ID: 5888 Superkingdom: Eukaryota Kingdom: not available Genus/species: Paramecium tetraurelia

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PT7-7

Entity Sequences (FASTA):

Entity Sequences (FASTA):
C-domain_of_Calmodulin_(residues_76-148): MKEQDSEEELIEAFKVFDRD GNGLISAAELRHVMTNLGEK LTDDEVDEMIREADIDGDGH INYEEFVRMMVSK
IQ_motif_peptide_of_NaV1-2_(residues_1901-1927): KRKQEEVSAIVIQRAYRRYL LKQKVKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	314
15N chemical shifts	78
1H chemical shifts	606

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	C-domain of Calmodulin	1
2	IQ motif peptide of NaV1.2	2
3	CALCIUM ION_1	3
4	CALCIUM ION_2	3

Entities:

Entity 1, C-domain of Calmodulin 73 residues - 8416.369 Da.

1

MET

LYS

GLU

GLN

ASP

SER

GLU

LEU

2

ILE

GLU

ALA

PHE

LYS

VAL

PHE

ASP

ARG

ASP

3

GLY

ASN

GLY

LEU

ILE

SER

ALA

GLU

LEU

4

ARG

HIS

VAL

MET

THR

ASN

LEU

GLY

GLU

LYS

5

LEU

THR

ASP

GLU

VAL

ASP

GLU

MET

ILE

6

ARG

GLU

ALA

ASP

ILE

ASP

GLY

ASP

GLY

HIS

7

ILE

ASN

TYR

GLU

PHE

VAL

ARG

MET

8

VAL

SER

LYS

Entity 2, IQ motif peptide of NaV1.2 27 residues - 3370.125 Da.

peptide containing the IQ motif of the voltage dependent sodium channel NaV1.2

1

LYS

ARG

LYS

GLN

GLU

VAL

SER

ALA

ILE

2

VAL

ILE

GLN

ARG

ALA

TYR

ARG

TYR

LEU

3

LEU

LYS

GLN

LYS

VAL

LYS

Entity 3, CALCIUM ION_1 - Ca - 40.078 Da.

1

CA

Samples:

sample_1: C-domain of Calmodulin, [U-100% 13C; U-100% 15N], 1.5 mM; IQ motif peptide of NaV1.2 1.5 mM; CALCIUM ION 3.3 mM; imidazole, [U-2H], 10 mM; potassium chloride 100 mM; sodium azide 0.01%; EDTA, [U-2H], 50 uM; H2O 95%; D2O 5%

sample_2: C-domain of Calmodulin, [U-100% 13C; U-100% 15N], 1.5 mM; IQ motif peptide of NaV1.2 1.5 mM; CALCIUM ION 3.3 mM; imidazole, [U-2H], 10 mM; potassium chloride 100 mM; sodium azide 0.01%; EDTA, [U-2H], 50 uM; D2O 100%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D H(C)CH-TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
3D 1H-13C edited, 12C filtered NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H doubly 12C,14N filtered NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H 12C,14N filtered TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H 12C filtered NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H 12C,14N filtered TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection

SPARKY v3.115, Goddard - chemical shift assignment, data analysis, peak picking

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

Analysis v2.1.5, CCPN - chemical shift assignment, data analysis, peak picking

ARIA v2.3, Linge, O'Donoghue and Nilges - data analysis, structure solution

CNSSOLVE v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - data analysis, refinement, structure solution

X-PLOR NIH v2.23, Schwieters, Kuszewski, Tjandra and Clore - data analysis, refinement, structure solution

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker Avance II 500 MHz
Bruker Avance II 800 MHz

NCBI	XP_001448363.1 NP_036779.1
UniProt	P04775.1
AlphaFold	P04775