BMRBj - BMREntryMaster

Found 1 Document (1.035 seconds)

BMRB: 17289

2L5Y

NMR structure of calcium-loaded STIM2 EF-SAM.

Authors

Zheng, L., Stathopulos, P.B., Ikura, M.

Assembly

Stromal Interaction Molecule 2

Entity

1. Stromal Interaction Molecule 2 (polymer, Thiol state: not present), 150 monomers, 17800.70 Da Detail

GSHMASTEED RFSLEALQTI HKQMDDDKDG GIEVEESDEF IREDMKYKDA TNKHSHLHRE DKHITIEDLW KRWKTSEVHN WTLEDTLQWL IEFVELPQYE KNFRDNNVKG TTLPRIAVHE PSFMISQLKI SDRSHRQKLQ LKALDVVLFG

2. CA (non-polymer, Thiol state: not present), 40.078 Da

Total weight

17840.777 Da

Max. entity weight

17800.7 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 77.7 %, Completeness (bb): 79.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.7 % (1416 of 1823)	84.5 % (807 of 955)	65.7 % (463 of 705)	89.6 % (146 of 163)
Backbone	79.0 % (706 of 894)	90.7 % (274 of 302)	66.7 % (297 of 445)	91.8 % (135 of 147)
Sidechain	78.5 % (843 of 1074)	81.6 % (533 of 653)	73.8 % (299 of 405)	68.8 % (11 of 16)
Aromatic	30.0 % (48 of 160)	55.0 % (44 of 80)	0.0 % (0 of 76)	100.0 % (4 of 4)
Methyl	97.3 % (144 of 148)	95.9 % (71 of 74)	98.6 % (73 of 74)

1. Stromal Interaction Molecule 2

GSHMASTEED RFSLEALQTI HKQMDDDKDG GIEVEESDEF IREDMKYKDA TNKHSHLHRE DKHITIEDLW KRWKTSEVHN WTLEDTLQWL IEFVELPQYE KNFRDNNVKG TTLPRIAVHE PSFMISQLKI SDRSHRQKLQ LKALDVVLFG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 15N]	0.5 ~ 0.7 mM
2	TRIS	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	Calcium Ion	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
13	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
14	TRIS	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	CALCIUM ION	natural abundance	10 mM
17	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L5Y, Strand ID: A Detail

Release date

2011-01-17

Citation

Auto-inhibitory role of the EF-SAM domain of STIM proteins in store-operated calcium entry
Zheng, L., Stathopulos, P.B., Schindl, R., Li, G., Romanin, C., Ikura, M.
Proc. Natl. Acad. Sci. U. S. A. (2011), 108, 1337-1342, PubMed 21217057 , DOI 10.1073/pnas.1015125108 , Abstract

Related entities 1. Stromal Interaction Molecule 2, : 1 : 2 : 20 entities Detail

Interaction partners 1. Stromal Interaction Molecule 2, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 15N]	0.5 ~ 0.7 mM
2	TRIS	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	Calcium Ion	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 15N]	0.5 ~ 0.7 mM
2	TRIS	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	Calcium Ion	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K

#	Name	Isotope labeling	Concentration
13	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
14	TRIS	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	CALCIUM ION	natural abundance	10 mM
17	D2O	natural abundance	100 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	Calcium Ion	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

10 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K

#	Name	Isotope labeling	Concentration
13	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
14	TRIS	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	CALCIUM ION	natural abundance	10 mM
17	D2O	natural abundance	100 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K

#	Name	Isotope labeling	Concentration
13	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
14	TRIS	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	CALCIUM ION	natural abundance	10 mM
17	D2O	natural abundance	100 %

12 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K

#	Name	Isotope labeling	Concentration
13	PROTEIN (Stromal Interaction Molecule 2)	[U-99% 13C; U-99% 15N]	0.5 ~ 0.7 mM
14	TRIS	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	CALCIUM ION	natural abundance	10 mM
17	D2O	natural abundance	100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17289_2l5y.nef
Input source #2: Coordindates	2l5y.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:36:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:33:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:29:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:36:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:31:GLY:O	2:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-------------70--------80--------90-------100-------110-------120-------130-------140-------150-----
GSHMASTEEDRFSLEALQTIHKQMDDDKDGGIEVEESDEFIREDMKYKDATNKHSHLHREDKHITIEDLWKRWKTSEVHNWTLEDTLQWLIEFVELPQYE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMASTEEDRFSLEALQTIHKQMDDDKDGGIEVEESDEFIREDMKYKDATNKHSHLHREDKHITIEDLWKRWKTSEVHNWTLEDTLQWLIEFVELPQYE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--160-------170-------180-------190-------200-----
KNFRDNNVKGTTLPRIAVHEPSFMISQLKISDRSHRQKLQLKALDVVLFG
||||||||||||||||||||||||||||||||||||||||||||||||||
KNFRDNNVKGTTLPRIAVHEPSFMISQLKISDRSHRQKLQLKALDVVLFG
-------110-------120-------130-------140-------150

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	150	0	0	100.0

Content subtype: combined_17289_2l5y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1377		96.7 (chain: A, length: 150)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	8605 (1)	noe	94.0 (chain: A, length: 150)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	91 (1)	hbond	49.3 (chain: A, length: 150)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	91 (1)	hbond	49.3 (chain: A, length: 150)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	176 (176)	.	74.0 (chain: A, length: 150)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	176 (176)	.	74.0 (chain: A, length: 150)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 150, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 805
  - ¹⁵N chemical shifts: 141
  - ¹³C chemical shifts: 431
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	955	804	84.2
¹⁵N chemical shifts	171	141	82.5
¹³C chemical shifts	705	431	61.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	302	272	90.1
¹⁵N chemical shifts	147	131	89.1
¹³C chemical shifts	300	136	45.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	653	532	81.5
¹⁵N chemical shifts	24	10	41.7
¹³C chemical shifts	405	295	72.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	76	97.4
¹³C chemical shifts	78	76	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	44	55.0
¹⁵N chemical shifts	4	4	100.0
¹³C chemical shifts	76	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 150, Sequence coverage: 94.0%
- Total number of restraints: 8605
- Weight of restraints: 1.0 (8605)
- Potential type of restraints: square-well-parabolic (8605)
- Range of distance target values: 1.17, 3.07 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 150, Sequence coverage: 49.3%
  - Total number of restraints: 91
  - Weight of restraints: 1.0 (91)
  - Potential type of restraints: square-well-parabolic (91)
  - Range of distance target values: 1.0, 1.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 150, Sequence coverage: 49.3%
    - Total number of restraints: 91
    - Weight of restraints: 1.0 (91)
    - Potential type of restraints: square-well-parabolic (91)
    - Range of distance target values: 1.0, 1.5 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 150, Sequence coverage: 74.0%
- Total number of restraints: 176
- Total number of restraints per polymer type: 176
- Weight of restraints: 1.0 (176)
- Potential type of restraints: square-well-parabolic (176)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 150, Sequence coverage: 74.0%
  - Total number of restraints: 176
  - Total number of restraints per polymer type: 176
  - Weight of restraints: 1.0 (176)
  - Potential type of restraints: square-well-parabolic (176)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords EF-hand, NMR, SAM domain, stromal interaction molecule

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.035 seconds)

BMRB: 17289

Sample #1

Sample #2

Sample #3

Related entities 1. Stromal Interaction Molecule 2, : 1 : 2 : 20 entities Detail

Interaction partners 1. Stromal Interaction Molecule 2, : 5 interactors Detail

Experiments performed 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail