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- PDB-2l5y: NMR structure of calcium-loaded STIM2 EF-SAM. -

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Basic information

Entry
Database: PDB / ID: 2l5y
TitleNMR structure of calcium-loaded STIM2 EF-SAM.
ComponentsStromal interaction molecule 2
KeywordsSIGNALING PROTEIN / stromal interaction molecule / EF-hand / SAM domain / store operated calcium entry
Function / homology
Function and homology information


store-operated calcium entry / activation of store-operated calcium channel activity / store-operated calcium channel activity / positive regulation of calcium ion transport / calcium channel regulator activity / intracellular calcium ion homeostasis / membrane => GO:0016020 / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Stromal interaction molecule 2, SAM domain / Recoverin; domain 1 - #180 / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif domain / Recoverin; domain 1 ...Stromal interaction molecule 2, SAM domain / Recoverin; domain 1 - #180 / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif domain / Recoverin; domain 1 / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Stromal interaction molecule 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsZheng, L. / Stathopulos, P.B. / Ikura, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Auto-inhibitory role of the EF-SAM domain of STIM proteins in store-operated calcium entry.
Authors: Zheng, L. / Stathopulos, P.B. / Schindl, R. / Li, G.Y. / Romanin, C. / Ikura, M.
History
DepositionNov 9, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stromal interaction molecule 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8712
Polymers17,8311
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Stromal interaction molecule 2


Mass: 17830.967 Da / Num. of mol.: 1 / Fragment: UNP residues 62-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1482, STIM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P246
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structural ensemble of the calcium sensing region of stromal interaction molecule-2 consisting of the EF-hand together with the SAM domains (residues 62-205).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HN(CA)CB
1413D 1H-15N NOESY
2533D 1H-13C NOESY
1623D HN(CO)CA
1723D HNCA
1823D HNCO
1923D HBHA(CO)NH
21032D 1H-13C HSQC
21133D (H)CCH-TOCSY
21233D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.7 mM [U-99% 15N] PROTEIN (Stromal Interaction Molecule 2)-1, 20 mM TRIS-2, 100 mM sodium chloride-3, 10 mM Calcium Ion-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5-0.7 mM [U-99% 13C; U-99% 15N] PROTEIN (Stromal Interaction Molecule 2)-5, 20 mM TRIS-6, 100 mM sodium chloride-7, 10 mM Calcium Ion-8, 90% H2O/10% D2O90% H2O/10% D2O
30.5-0.7 mM [U-99% 13C; U-99% 15N] PROTEIN (Stromal Interaction Molecule 2)-9, 20 mM TRIS-10, 100 mM sodium chloride-11, 10 mM CALCIUM ION-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPROTEIN (Stromal Interaction Molecule 2)-1[U-99% 15N]0.5-0.71
20 mMTRIS-21
100 mMsodium chloride-31
10 mMCalcium Ion-41
mMPROTEIN (Stromal Interaction Molecule 2)-5[U-99% 13C; U-99% 15N]0.5-0.72
20 mMTRIS-62
100 mMsodium chloride-72
10 mMCalcium Ion-82
mMPROTEIN (Stromal Interaction Molecule 2)-9[U-99% 13C; U-99% 15N]0.5-0.73
20 mMTRIS-103
100 mMsodium chloride-113
10 mMCALCIUM ION-123
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1105 7.5 ambient 288 K
2105 ambient 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSv1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAv2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
Details: Water refinement was performed using the RECOORD scripts (Nederveen et al., 2005) in CNS (v1.1) (Brunger et al., 1998)., Water refinement was performed using the RECOORD scripts (Nederveen ...Details: Water refinement was performed using the RECOORD scripts (Nederveen et al., 2005) in CNS (v1.1) (Brunger et al., 1998)., Water refinement was performed using the RECOORD scripts (Nederveen et al., 2005) in CNS (v1.1) (Brunger et al., 1998).
NMR constraintsNOE constraints total: 2714 / NOE intraresidue total count: 757 / NOE long range total count: 617 / NOE medium range total count: 667 / NOE sequential total count: 667 / Hydrogen bond constraints total count: 91 / Protein phi angle constraints total count: 88 / Protein psi angle constraints total count: 88
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.1162 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 6.251 ° / Maximum upper distance constraint violation: -4.19 Å
Torsion angle constraint violation method: Violation analysis scripts from RECOORD in CNS.
NMR ensemble rmsDistance rms dev: 0.0296 Å / Distance rms dev error: 0.0134 Å

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