BMRB Entry 15851

Name: NMR structure of calcium-loaded STIM1 EF-SAM
Published: 2008-10-14

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PDB ID: 2k60
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15851
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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:

NMR structure of calcium-loaded STIM1 EF-SAM

Deposition date:

2008-07-02

Original release date:

2008-10-14

Authors:

Stathopulos, Peter; Ikura, Mitsuhiko

Citation:

Citation: Stathopulos, Peter; Zheng, Le; Li, Guang-Yao; Plevin, Michael; Ikura, Mitsuhiko. "Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry" Cell 135, 110-122 (2008).
PubMed: 18854159

Assembly members:

Assembly members:
stromal_interaction_molecule_1, polymer, 150 residues, 17380.514 Da.
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 Vector: pET-28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
stromal_interaction_molecule_1: GSHMASSEDEKLSFEAVRNI HKLMDDDANGDVDVEESDEF LREDLNYHDPTVKHSTFHGE DKLISVEDLWKAWKSSEVYN WTVDEVVQWLITYVELPQYE ETFRKLQLSGHAMPRLAVTN TTMTGTVLKMTDRSHRQKLQ LKALDTVLFG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	569
15N chemical shifts	125
1H chemical shifts	978

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Stromal interaction molecule 1	1
2	CALCIUM ION	2

Entities:

Entity 1, Stromal interaction molecule 1 150 residues - 17380.514 Da.

The first 6 residues (numbered -5, -4, -3, -2, -1, 0) are remnants of the non-native affinity tag. The remaining residues are situated in the endoplasmic reticulum luminal portion of STIM1 (58 to 201).

1	GLY	SER	HIS	MET	ALA	SER	SER	GLU	ASP	GLU
2	LYS	LEU	SER	PHE	GLU	ALA	VAL	ARG	ASN	ILE
3	HIS	LYS	LEU	MET	ASP	ASP	ASP	ALA	ASN	GLY
4	ASP	VAL	ASP	VAL	GLU	GLU	SER	ASP	GLU	PHE
5	LEU	ARG	GLU	ASP	LEU	ASN	TYR	HIS	ASP	PRO
6	THR	VAL	LYS	HIS	SER	THR	PHE	HIS	GLY	GLU
7	ASP	LYS	LEU	ILE	SER	VAL	GLU	ASP	LEU	TRP
8	LYS	ALA	TRP	LYS	SER	SER	GLU	VAL	TYR	ASN
9	TRP	THR	VAL	ASP	GLU	VAL	VAL	GLN	TRP	LEU
10	ILE	THR	TYR	VAL	GLU	LEU	PRO	GLN	TYR	GLU
11	GLU	THR	PHE	ARG	LYS	LEU	GLN	LEU	SER	GLY
12	HIS	ALA	MET	PRO	ARG	LEU	ALA	VAL	THR	ASN
13	THR	THR	MET	THR	GLY	THR	VAL	LEU	LYS	MET
14	THR	ASP	ARG	SER	HIS	ARG	GLN	LYS	LEU	GLN
15	LEU	LYS	ALA	LEU	ASP	THR	VAL	LEU	PHE	GLY

Entity 2, CALCIUM ION - Ca - 40.078 Da.

1

CA

Samples:

sample_1: stromal interaction molecule 1, [U-100% 13C; U-100% 15N], 0.5-1.0 mM; TRIS 20 mM; sodium chloride 100 mM; CALCIUM ION 5 mM

sample_2: stromal interaction molecule 1, [U-100% 13C; U-100% 15N], 0.5-1.0 mM; TRIS, [U-99% 2H], 20 mM; sodium chloride 100 mM; CALCIUM ION 5 mM

sample_condition_1: ionic strength: 105 mM; pH: 8.0; pressure: 1 atm; temperature: 293 K

sample_condition_2: ionic strength: 105 mM; pD: 8.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_condition_1
3D CBCA(CO)NH	sample_1	isotropic	sample_condition_1
3D HNCACB	sample_1	isotropic	sample_condition_1
3D HNCO	sample_1	isotropic	sample_condition_1
3D H(CCO)NH	sample_1	isotropic	sample_condition_1
3D C(CO)NH	sample_1	isotropic	sample_condition_1
3D 1H-15N NOESY	sample_1	isotropic	sample_condition_1
3D HCCH-TOCSY	sample_2	isotropic	sample_condition_2
2D 1H-13C HSQC	sample_2	isotropic	sample_condition_2
3D 1H-13C NOESY	sample_2	isotropic	sample_condition_2

Software:

CNS vv1.1, Brunger A. T. et.al. - refinement

CYANA vv2.1, Guntert, Mumenthaler and Wuthrich - structure solution

XEASY, Bartels et al. - chemical shift assignment

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

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz

PDB	2K60
DBJ	BAG54839
GB	AAC51627 AAH21300 ABM86435 ABW03792 ADO20317
REF	NP_001248464 NP_001264890 NP_001264891 NP_003147 XP_001160553
SP	Q13586
AlphaFold	Q13586

1	GLY	SER	HIS	MET	ALA	SER	SER	GLU	ASP	GLU
2	LYS	LEU	SER	PHE	GLU	ALA	VAL	ARG	ASN	ILE
3	HIS	LYS	LEU	MET	ASP	ASP	ASP	ALA	ASN	GLY
4	ASP	VAL	ASP	VAL	GLU	GLU	SER	ASP	GLU	PHE
5	LEU	ARG	GLU	ASP	LEU	ASN	TYR	HIS	ASP	PRO
6	THR	VAL	LYS	HIS	SER	THR	PHE	HIS	GLY	GLU
7	ASP	LYS	LEU	ILE	SER	VAL	GLU	ASP	LEU	TRP
8	LYS	ALA	TRP	LYS	SER	SER	GLU	VAL	TYR	ASN
9	TRP	THR	VAL	ASP	GLU	VAL	VAL	GLN	TRP	LEU
10	ILE	THR	TYR	VAL	GLU	LEU	PRO	GLN	TYR	GLU
11	GLU	THR	PHE	ARG	LYS	LEU	GLN	LEU	SER	GLY
12	HIS	ALA	MET	PRO	ARG	LEU	ALA	VAL	THR	ASN
13	THR	THR	MET	THR	GLY	THR	VAL	LEU	LYS	MET
14	THR	ASP	ARG	SER	HIS	ARG	GLN	LYS	LEU	GLN
15	LEU	LYS	ALA	LEU	ASP	THR	VAL	LEU	PHE	GLY

1	GLY	SER	HIS	MET	ALA	SER	SER	GLU	ASP	GLU
2	LYS	LEU	SER	PHE	GLU	ALA	VAL	ARG	ASN	ILE
3	HIS	LYS	LEU	MET	ASP	ASP	ASP	ALA	ASN	GLY
4	ASP	VAL	ASP	VAL	GLU	GLU	SER	ASP	GLU	PHE
5	LEU	ARG	GLU	ASP	LEU	ASN	TYR	HIS	ASP	PRO
6	THR	VAL	LYS	HIS	SER	THR	PHE	HIS	GLY	GLU
7	ASP	LYS	LEU	ILE	SER	VAL	GLU	ASP	LEU	TRP
8	LYS	ALA	TRP	LYS	SER	SER	GLU	VAL	TYR	ASN
9	TRP	THR	VAL	ASP	GLU	VAL	VAL	GLN	TRP	LEU
10	ILE	THR	TYR	VAL	GLU	LEU	PRO	GLN	TYR	GLU
11	GLU	THR	PHE	ARG	LYS	LEU	GLN	LEU	SER	GLY
12	HIS	ALA	MET	PRO	ARG	LEU	ALA	VAL	THR	ASN
13	THR	THR	MET	THR	GLY	THR	VAL	LEU	LYS	MET
14	THR	ASP	ARG	SER	HIS	ARG	GLN	LYS	LEU	GLN
15	LEU	LYS	ALA	LEU	ASP	THR	VAL	LEU	PHE	GLY