BMRB Entry 34496

Name: Ca2+-bound Calmodulin mutant N53I
Published: 2020-04-27

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PDB ID: 6y94
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34496
MolProbity Validation Chart

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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:

Ca2+-bound Calmodulin mutant N53I

Deposition date:

2020-03-06

Original release date:

2020-04-27

Authors:

Holt, C.; Nielsen, L.; Lau, K.; Brohus, M.; Sorensen, A.; Larsen, K.; Sommer, C.; Petegem, F.; Overgaard, M.; Wimmer, R.

Citation:

Citation: Holt, C.; Hamborg, L.; Lau, K.; Brohus, M.; Sorensen, A.; Larsen, K.; Sommer, C.; Petegem, F.; Overgaard, M.; Wimmer, R.. "The arrhythmogenic N53I variant subtly changes the structure and dynamics in the calmodulin N-domain, altering its interaction with the cardiac ryanodine receptor" J. Biol. Chem. 295, 7620-7634 (2020).
PubMed: 32317284

Assembly members:

Assembly members:
entity_1, polymer, 148 residues, 16720.404 Da.
entity_CA, non-polymer, 40.078 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ADQLTEEQIAEFKEAFSLFD KDGDGTITTKELGTVMRSLG QNPTEAELQDMIIEVDADGN GTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEE FVQMMTAK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1

Data type	Count
13C chemical shifts	631
15N chemical shifts	157
1H chemical shifts	992
T1 relaxation values	141
T2 relaxation values	143
heteronuclear NOE values	143

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	2
4	unit_4	2
5	unit_5	2

Entities:

Entity 1, unit_1 148 residues - 16720.404 Da.

1

ALA

ASP

GLN

LEU

THR

GLU

GLN

ILE

ALA

2

GLU

PHE

LYS

GLU

ALA

PHE

SER

LEU

PHE

ASP

3

LYS

ASP

GLY

ASP

GLY

THR

ILE

THR

LYS

4

GLU

LEU

GLY

THR

VAL

MET

ARG

SER

LEU

GLY

5

GLN

ASN

PRO

THR

GLU

ALA

GLU

LEU

GLN

ASP

6

MET

ILE

GLU

VAL

ASP

ALA

ASP

GLY

ASN

7

GLY

THR

ILE

ASP

PHE

PRO

GLU

PHE

LEU

THR

8

MET

ALA

ARG

LYS

MET

LYS

ASP

THR

ASP

9

SER

GLU

ILE

ARG

GLU

ALA

PHE

ARG

10

VAL

PHE

ASP

LYS

ASP

GLY

ASN

GLY

TYR

ILE

11

SER

ALA

GLU

LEU

ARG

HIS

VAL

MET

THR

12

ASN

LEU

GLY

GLU

LYS

LEU

THR

ASP

GLU

13

VAL

ASP

GLU

MET

ILE

ARG

GLU

ALA

ASP

ILE

14

ASP

GLY

ASP

GLY

GLN

VAL

ASN

TYR

GLU

15

PHE

VAL

GLN

MET

THR

ALA

LYS

Entity 2, unit_2 - Ca - 40.078 Da.

1

CA

Samples:

sample_1: Calmodulin N53I, [U-99% 13C; U-99% 15N], 0.56 mM; HEPES 2 mM; potassium chloride 100 mM; calcium chloride 10 mM; sodium acetate 50 mM; sodium azide 2 mM; TSP 0.05 mM

sample_2: Calmodulin N53I, [U-99% 15N], 1.0 mM; HEPES 2 mM; potassium chloride 10 mM; calcium chloride 10 mM; sodium azide 2 mM; TSP 0.05 mM

sample_3: Calmodulin, [U-99% 13C; U-99% 15N], 1.0 mM; HEPES 2 mM; potassium chloride 10 mM; calcium chloride 10 mM; sodium azide 2 mM; TSP 0.05 mM

sample_conditions_1: ionic strength: 182 mM; pH: 6.57; pressure: 1 atm; temperature: 298.1 K

sample_conditions_2: ionic strength: 42 mM; pH: 6.57; pressure: 1 atm; temperature: 298.1 K

sample_conditions_3: ionic strength: 42 mM; pH: 6.57; pressure: 1 atm; temperature: 298.1 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCDCE)HE	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
{1H}-15N NOE	sample_2	isotropic	sample_conditions_2
15N-T2	sample_2	isotropic	sample_conditions_2
15N-T1	sample_2	isotropic	sample_conditions_2
T2 relaxation dispersion	sample_2	isotropic	sample_conditions_2
15N-T1	sample_3	isotropic	sample_conditions_3
15N-T2	sample_3	isotropic	sample_conditions_3
{1H}-15N NOE	sample_3	isotropic	sample_conditions_3
T2 relaxation dispersion	sample_3	isotropic	sample_conditions_3
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

YASARA v14.12.2, YASARA Biosciences GmbH - refinement

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

TALOS vTALOS+, Cornilescu, Delaglio and Bax - structure calculation

CARA v1.8.4.2, Keller and Wuthrich - chemical shift assignment, peak picking

TopSpin v3.2, Bruker Biospin - processing

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III HD 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks