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- PDB-2maj: Solution Structure of the STIM1 CC1-CC2 homodimer. -

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Basic information

Entry
Database: PDB / ID: 2maj
TitleSolution Structure of the STIM1 CC1-CC2 homodimer.
ComponentsStromal interaction molecule 1
KeywordsSIGNALING PROTEIN / STIM1 / coiled-coil / TRANSPORT PROTEIN
Function / homology
Function and homology information


store-operated calcium entry / activation of store-operated calcium channel activity / positive regulation of adenylate cyclase activity / regulation of store-operated calcium entry / enamel mineralization / cortical endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / microtubule plus-end binding / regulation of calcium ion transport / plasma membrane raft ...store-operated calcium entry / activation of store-operated calcium channel activity / positive regulation of adenylate cyclase activity / regulation of store-operated calcium entry / enamel mineralization / cortical endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / microtubule plus-end binding / regulation of calcium ion transport / plasma membrane raft / detection of calcium ion / Ion homeostasis / sarcoplasmic reticulum membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium channel regulator activity / positive regulation of angiogenesis / intracellular calcium ion homeostasis / protease binding / microtubule / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Stromal interaction molecule 1, SAM domain / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Stromal interaction molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsStathopulos, P.B. / Ikura, M.
CitationJournal: Nat Commun / Year: 2013
Title: STIM1/Orai1 coiled-coil interplay in the regulation of store-operated calcium entry.
Authors: Stathopulos, P.B. / Schindl, R. / Fahrner, M. / Zheng, L. / Gasmi-Seabrook, G.M. / Muik, M. / Romanin, C. / Ikura, M.
History
DepositionJul 12, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stromal interaction molecule 1
C: Stromal interaction molecule 1


Theoretical massNumber of molelcules
Total (without water)19,4062
Polymers19,4062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-33 kcal/mol
Surface area10070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Stromal interaction molecule 1


Mass: 9702.989 Da / Num. of mol.: 2 / Fragment: UNP residues 312-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STIM1, GOK / Production host: Escherichia coli (E. coli) / References: UniProt: Q13586

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D HNCO
1523D C(CO)NH TOCSY
1623D H(CCO)NH TOCSY
1713D 1H-15N NOESY
1832D 1H-13C HSQC
1933D 1H-13C NOESY
11043D 1H-13C-1H-12C/14N xfilt NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 15N] protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 100% D2O100% D2O
40.5 mM [U-99% 13C; U-99% 15N] protein, 0.5 mM protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-99% 15N]1
20 mMbis-TRIS-21
0.175 v/vTFE-3[U-99% 2H]1
0.5 mMentity-4[U-99% 13C; U-99% 15N]2
20 mMbis-TRIS-52
0.175 v/vTFE-6[U-99% 2H]2
0.5 mMentity-7[U-99% 13C; U-99% 15N]3
20 mMbis-TRIS-83
0.175 v/vTFE-9[U-99% 2H]3
0.5 mMentity-10[U-99% 13C; U-99% 15N]4
0.5 mMentity-114
20 mMbis-TRIS-124
0.175 v/vTFE-13[U-99% 2H]4
Sample conditionsIonic strength: 0.02 / pH: 5.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Used the RECOORD scripts in CNS to water refine the CYANA-determined structures (Nederveen et al., Proteins. 2005 Jun 1;59(4):662-72).
NMR constraintsNOE constraints total: 2199 / NOE intraresidue total count: 578 / NOE long range total count: 474 / NOE medium range total count: 643 / NOE sequential total count: 504 / Hydrogen bond constraints total count: 236 / Protein phi angle constraints total count: 134 / Protein psi angle constraints total count: 134
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.94 ° / Maximum upper distance constraint violation: -0.24 Å
Torsion angle constraint violation method: RECOORD in CNS (Proteins. 2005 Jun 1;59(4):662-72)
NMR ensemble rmsDistance rms dev: 0.024 Å / Distance rms dev error: 0.001 Å

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