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- PDB-2kle: ISIC Refined Solution Structure of the Calcium Binding Domain of ... -

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Entry
Database: PDB / ID: 2kle
TitleISIC Refined Solution Structure of the Calcium Binding Domain of the C-terminal Cytosolic Domain of Polycystin-2
ComponentsPolycystin-2
KeywordsMEMBRANE PROTEIN / PC2 / PKD2 / Calcium binding domain / EF hand / Cytosolic / Calcium / Coiled coil / Disease mutation / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Polymorphism / Transmembrane / Transport
Function / homology
Function and homology information


detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / basal cortex / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / calcium-induced calcium release activity / voltage-gated monoatomic ion channel activity / muscle alpha-actinin binding / cation channel complex / regulation of calcium ion import / placenta blood vessel development / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / cellular response to fluid shear stress / non-motile cilium / cellular response to osmotic stress / actinin binding / voltage-gated monoatomic cation channel activity / motile cilium / transcription regulator inhibitor activity / aorta development / determination of left/right symmetry / inorganic cation transmembrane transport / neural tube development / voltage-gated sodium channel activity / ciliary membrane / protein heterotetramerization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / negative regulation of ryanodine-sensitive calcium-release channel activity / cytoplasmic side of endoplasmic reticulum membrane / centrosome duplication / cell surface receptor signaling pathway via JAK-STAT / voltage-gated potassium channel activity / potassium channel activity / embryonic placenta development / voltage-gated calcium channel activity / sodium ion transmembrane transport / monoatomic cation channel activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / cytoskeletal protein binding / potassium ion transmembrane transport / cellular response to calcium ion / basal plasma membrane / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / protein tetramerization / calcium ion transmembrane transport / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / intracellular calcium ion homeostasis / cellular response to reactive oxygen species / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / heart development / regulation of cell population proliferation / ATPase binding / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / EF-hand / Recoverin; domain 1 ...Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsKalbitzer, H.R.
Citation
Journal: Biomol.Nmr Assign. / Year: 2009
Title: NMR-assignments of a cytosolic domain of the C-terminus of polycystin-2
Authors: Schumann, F.H. / Hoffmeister, H. / Schmidt, M. / Bader, R. / Besl, E. / Witzgall, R. / Kalbitzer, H.R.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Ca2+-dependent conformational changes in a C-terminal cytosolic domain of polycystin-2
Authors: Schumann, F. / Hoffmeister, H. / Bader, R. / Schmidt, M. / Witzgall, R. / Kalbitzer, H.R.
History
DepositionJul 1, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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
A: Polycystin-2


Theoretical massNumber of molelcules
Total (without water)14,0241
Polymers14,0241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Polycystin-2 / Polycystic kidney disease 2 protein / Autosomal dominant polycystic kidney disease type II protein ...Polycystic kidney disease 2 protein / Autosomal dominant polycystic kidney disease type II protein / Polycystwin / R48321


Mass: 14024.415 Da / Num. of mol.: 1 / Fragment: residues 680-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13563

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCANNH
1613D HNCO
1712D 15N-TOCSY-HSQC
1813D (H)CCH-TOCSY
1912D 1H-1H NOESY
11013D 1H-15N-NOESY-HSQC

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Sample preparation

DetailsContents: 0.5mM [U-100% 13C; U-100% 15N] Polycystin-2 Polypeptide-1, 5mM Ca2+-2, 0.1mM DSS-3, 10mM potassium phosphate buffer-4, 500mM NaCl-5, 2mM DTE-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPolycystin-2 Polypeptide-1[U-100% 13C; U-100% 15N]1
5 mMCa2+-21
0.1 mMDSS-31
10 mMpotassium phosphate buffer-41
500 mMNaCl-51
2 mMDTE-61
Sample conditionsIonic strength: 0.51 / pH: 6.8 / Pressure: ambient / Temperature: 293 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
AUREMOLBruker Biospinchemical shift assignment
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospindata analysis
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Auremol-ISICBrunner, K., Gronwald, W., Trenner, J.M., Neidig, K.P., and Kalbitzer, H.R.refinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE FIRST REFINED WITH AUREMOL-ISUC AND THEN REFINED WITH CNS IN EXPLICIT WATER; Brunner, K., Gronwald, W., Trenner, J.M., Neidig, K.P., and Kalbitzer, H.R. (2006) BMC Struct. ...Details: THE STRUCTURES WERE FIRST REFINED WITH AUREMOL-ISUC AND THEN REFINED WITH CNS IN EXPLICIT WATER; Brunner, K., Gronwald, W., Trenner, J.M., Neidig, K.P., and Kalbitzer, H.R. (2006) BMC Struct. Biol. 6, 14, for Waterre finement; Linge, J.P., Williams, M.A., Spronk, C.A.E.M., Bonvin, A.M.J.J. & Nilges, M. (2003). Refinement of protein structures in explicit solvent. Proteins: Struct. Funct. Genet. 50, 496-506 for EXPLICIT WATER refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10 / Representative conformer: 1

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