BMRB Entry 31155

Name: Solution NMR structure of the human LETM1 F-EF-hand domain in the presence of calcium
Published: 2024-10-15

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PDB ID: 9ba1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31155
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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:

Solution NMR structure of the human LETM1 F-EF-hand domain in the presence of calcium

Deposition date:

2024-04-03

Original release date:

2024-10-15

Authors:

Lin, Q.; Stathopulos, P.

Citation:

Citation: Lin, Qi-Tong; Colussi, Danielle; Lake, Taylor; Stathopulos, Peter. "An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium" Structure ., .-. (2024).
PubMed: 39317198

Assembly members:

Assembly members:
entity_1, polymer, 63 residues, 6781.691 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHMASTGENVISVAELINA MKQVKHIPESKLTSLAAALD ENKDGKVNIDDLVKVIELVD KED

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	244
15N chemical shifts	54
1H chemical shifts	422

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

Entities:

Entity 1, unit_1 63 residues - 6781.691 Da.

1

GLY

SER

HIS

MET

ALA

SER

THR

GLY

GLU

ASN

2

VAL

ILE

SER

VAL

ALA

GLU

LEU

ILE

ASN

ALA

3

MET

LYS

GLN

VAL

LYS

HIS

ILE

PRO

GLU

SER

4

LYS

LEU

THR

SER

LEU

ALA

LEU

ASP

5

GLU

ASN

LYS

ASP

GLY

LYS

VAL

ASN

ILE

ASP

6

ASP

LEU

VAL

LYS

VAL

ILE

GLU

LEU

VAL

ASP

7

LYS

GLU

ASP

Entity 2, unit_2 - Ca - 40.078 Da.

1

CA

Samples:

sample_1: Mitochondrial proton/calcium exchanger protein, [U-99% 15N], 1 mM; TRIS 20 mM; sodium chloride 50 mM; CHAPS 10 mM; calcium chloride 30 mM

sample_2: Mitochondrial proton/calcium exchanger protein, [U-99% 13C; U-99% 15N], 1 mM; TRIS 20 mM; sodium chloride 50 mM; CHAPS 10 mM; calcium chloride 30 mM

sample_3: Mitochondrial proton/calcium exchanger protein, [U-99% 13C; U-99% 15N], 1 mM; TRIS 20 mM; sodium chloride 50 mM; CHAPS 10 mM; calcium chloride 30 mM

sample_conditions_1: ionic strength: 140 mM; pH: 7.8; pressure: 1 atm; temperature: 308.15 K

sample_conditions_2: ionic strength: 140 mM; pH: 8.2 pD; pressure: 1 atm; temperature: 308.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_2
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

CARA v1.9.1b12, Keller and Wuthrich - chemical shift assignment

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

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 600 MHz

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