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- PDB-2k60: NMR structure of calcium-loaded STIM1 EF-SAM -

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Basic information

Entry
Database: PDB / ID: 2k60
TitleNMR structure of calcium-loaded STIM1 EF-SAM
ComponentsPROTEIN (Stromal interaction molecule 1)
KeywordsSIGNALING PROTEIN / EF-hand / SAM domain / EF-SAM / STIM1 / stromal interaction molecule / store operated calcium entry regulator / SOCE / endoplasmic reticulum luminal calcium sensor / Calcium transport / Glycoprotein / Ion transport / Membrane / Phosphoprotein / Transmembrane / Transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


store-operated calcium entry / activation of store-operated calcium channel activity / regulation of store-operated calcium entry / enamel mineralization / Elevation of cytosolic Ca2+ levels / cortical endoplasmic reticulum / positive regulation of adenylate cyclase activity / microtubule plus-end binding / plasma membrane raft / regulation of calcium ion transport ...store-operated calcium entry / activation of store-operated calcium channel activity / regulation of store-operated calcium entry / enamel mineralization / Elevation of cytosolic Ca2+ levels / cortical endoplasmic reticulum / positive regulation of adenylate cyclase activity / microtubule plus-end binding / plasma membrane raft / regulation of calcium ion transport / calcium channel regulator activity / detection of calcium ion / Ion homeostasis / sarcoplasmic reticulum membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / intracellular calcium ion homeostasis / positive regulation of angiogenesis / microtubule / protease binding / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Recoverin; domain 1 - #180 / Stromal interaction molecule 1, SAM domain / 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. / Sterile alpha motif domain ...Recoverin; domain 1 - #180 / Stromal interaction molecule 1, SAM domain / 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. / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailsEF-hand and SAM domain structural organization for calcium-loaded stromal interaction molecule 1
AuthorsStathopulos, P.B. / Ikura, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural and mechanistic insights into STIM1-mediated initiation of store-operated calcium entry.
Authors: Stathopulos, P.B. / Zheng, L. / Li, G.Y. / Plevin, M.J. / Ikura, M.
History
DepositionJul 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Database references
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_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _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_ref_seq_dif.details / _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: PROTEIN (Stromal interaction molecule 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4202
Polymers17,3801
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PROTEIN (Stromal interaction molecule 1)


Mass: 17380.375 Da / Num. of mol.: 1 / Fragment: UNP residues 58-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STIM1, GOK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13586
#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: EF-hand and SAM domain structural organization for calcium-loaded stromal interaction molecule 1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D H(CCO)NH
1613D C(CO)NH
1713D 1H-15N NOESY
2823D (H)CCH-TOCSY
2922D 1H-13C HSQC
21023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM [U-100% 13C; U-100% 15N] stromal interaction molecule 1, 20 mM TRIS, 100 mM sodium chloride, 5 mM CALCIUM ION, 95% H2O/5% D2O95% H2O/5% D2O
20.5-1.0 mM [U-100% 13C; U-100% 15N] stromal interaction molecule 1, 20 mM [U-99% 2H] TRIS, 100 mM sodium chloride, 5 mM CALCIUM ION, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMstromal interaction molecule 1[U-100% 13C; U-100% 15N]1
20 mMTRIS1
100 mMsodium chloride1
5 mMCALCIUM ION1
0.5 mMstromal interaction molecule 1[U-100% 13C; U-100% 15N]2
20 mMTRIS[U-99% 2H]2
100 mMsodium chloride2
5 mMCALCIUM ION2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1105 8.0 1 atm293 K
2105 1 atm293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSv1.1Brunger A. T. et.al.refinement
CYANAv2.1Guntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1
Details: Water refinement and violation analysis was performed using the RECOORD scripts in CNS v1.1 (Nederveen et al, 2005).
NMR constraintsNOE constraints total: 3066 / NOE intraresidue total count: 796 / NOE long range total count: 802 / NOE medium range total count: 781 / NOE sequential total count: 687 / Hydrogen bond constraints total count: 106 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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