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- PDB-2k2f: Solution structure of Ca2+-S100A1-RyRP12 -

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Basic information

Entry
Database: PDB / ID: 2k2f
TitleSolution structure of Ca2+-S100A1-RyRP12
Components
  • Protein S100-A1
  • Ryanodine receptor 1 peptide
KeywordsMETAL BINDING PROTEIN / S100 / EF hand / ryanodine receptor / calcium binding / Alternative splicing / Calcium channel / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Polymorphism / Transmembrane / Transport / Cytoplasm / Metal-binding / Zinc
Function / homology
Function and homology information


Stimuli-sensing channels / Regulation of TLR by endogenous ligand / manganese ion transmembrane transport / positive regulation of voltage-gated calcium channel activity / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / regulation of catalytic activity / left ventricular cardiac muscle tissue morphogenesis / suramin binding ...Stimuli-sensing channels / Regulation of TLR by endogenous ligand / manganese ion transmembrane transport / positive regulation of voltage-gated calcium channel activity / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / regulation of catalytic activity / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / sarcoplasmic reticulum calcium ion transport / regulation of SA node cell action potential / calcium-induced calcium release activity / calcium ion transport into cytosol / A band / embryonic heart tube morphogenesis / ventricular cardiac muscle cell action potential / cardiac muscle hypertrophy / regulation of ventricular cardiac muscle cell action potential / S100 protein binding / M band / ryanodine-sensitive calcium-release channel activity / response to redox state / regulation of heart contraction / voltage-gated calcium channel complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / response to caffeine / regulation of cardiac muscle contraction by calcium ion signaling / I band / extrinsic component of cytoplasmic side of plasma membrane / response to muscle activity / cellular response to caffeine / calcium ion transmembrane import into cytosol / positive regulation of sprouting angiogenesis / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / negative regulation of cytosolic calcium ion concentration / positive regulation of the force of heart contraction / smooth endoplasmic reticulum / response to muscle stretch / intracellularly gated calcium channel activity / response to magnesium ion / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cytosolic calcium ion concentration / positive regulation of heart rate / ATP metabolic process / cardiac muscle contraction / release of sequestered calcium ion into cytosol / regulation of heart rate / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / response to nutrient / cellular response to epinephrine stimulus / calcium channel complex / sarcoplasmic reticulum membrane / calcium-mediated signaling / sarcomere / sarcoplasmic reticulum / striated muscle contraction / response to calcium ion / vasodilation / sarcolemma / intracellular calcium ion homeostasis / Z disc / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / calcium-dependent protein binding / nuclear envelope / ATPase binding / scaffold protein binding / monoatomic ion transmembrane transport / response to hypoxia / transmembrane transporter binding / calmodulin binding / response to xenobiotic stimulus / calcium ion binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat ...Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ryanodine receptor 2 / Protein S100-A1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailscalcium loaded S100A1 bound to a peptide from the calmodulin binding domain of RyR1
AuthorsWright, N.T. / Varney, K.M. / Weber, D.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: S100A1 and Calmodulin Compete for the Same Binding Site on Ryanodine Receptor.
Authors: Wright, N.T. / Prosser, B.L. / Varney, K.M. / Zimmer, D.B. / Schneider, M.F. / Weber, D.J.
History
DepositionApr 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Ryanodine receptor 1 peptide
D: Ryanodine receptor 1 peptide
A: Protein S100-A1
B: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9818
Polymers23,8214
Non-polymers1604
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Ryanodine receptor 1 peptide


Mass: 1470.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RYR1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS(DE3) / References: UniProt: B0LPN4*PLUS
#2: Protein Protein S100-A1 / S100 calcium-binding protein A1 / S-100 protein alpha subunit / S-100 protein alpha chain


Mass: 10439.614 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100a1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS(DE3) / References: UniProt: P35467
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: calcium loaded S100A1 bound to a peptide from the calmodulin binding domain of RyR1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D H(CCO)NH
1513D C(CO)NH
1612D 1H-1H TOCSY
1712D 1H-1H NOESY
1813D 13C ed 12C filt NOESY

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Sample preparation

DetailsContents: 10-15 mM CALCIUM ION, 1-3 mM [U-100% 13C; U-100% 15N] RYR1 peptide, 2-6 mM S100-A1 protein, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMCALCIUM ION1
1 mMentity_1[U-100% 13C; U-100% 15N]1
2 mMentity_21
10 %D2O1
Sample conditionsIonic strength: 40-50 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Zhengrong and Baxchemical shift assignment
NMRPipeDelaglio, Zhengrong and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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