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- PDB-2kq6: The structure of the EF-hand domain of polycystin-2 suggests a me... -

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Basic information

Entry
Database: PDB / ID: 2kq6
TitleThe structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity
ComponentsPolycystin-2Polycystin 2
KeywordsTRANSPORT PROTEIN / Protein X / 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 ...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 / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / 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 / regulation of calcium ion import / cation channel complex / calcium-induced calcium release activity / muscle alpha-actinin binding / placenta blood vessel development / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / voltage-gated monoatomic cation channel activity / non-motile cilium / cellular response to fluid shear stress / cellular response to osmotic stress / voltage-gated sodium channel activity / actinin binding / motile cilium / transcription regulator inhibitor activity / inorganic cation transmembrane transport / determination of left/right symmetry / aorta development / protein heterotetramerization / neural tube development / ciliary membrane / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / cytoplasmic side of endoplasmic reticulum membrane / voltage-gated potassium channel activity / potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / embryonic placenta development / cellular response to cAMP / release of sequestered calcium ion into cytosol / monoatomic cation channel activity / potassium ion transmembrane transport / cellular response to calcium ion / cytoskeletal protein binding / basal plasma membrane / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / protein tetramerization / phosphoprotein binding / calcium ion transmembrane transport / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / intracellular calcium ion homeostasis / cellular response to reactive oxygen species / positive regulation of nitric oxide biosynthetic process / calcium ion transport / cell-cell junction / lamellipodium / regulation of cell population proliferation / heart development / ATPase binding / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / 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 / Polycystin domain / Polycystin domain / Polycystic kidney disease type 2 protein / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. ...Ferredoxin I 4Fe-4S cluster domain / Polycystin domain / Polycystin domain / Polycystic kidney disease type 2 protein / 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 / XPLOR-NIH
AuthorsPetri, E.T. / Celic, A. / Kennedy, S.D. / Ehrlich, B.E. / Boggon, T.J. / Hodsdon, M.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity.
Authors: Petri, E.T. / Celic, A. / Kennedy, S.D. / Ehrlich, B.E. / Boggon, T.J. / Hodsdon, M.E.
History
DepositionOct 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)9,0101
Polymers9,0101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy and least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Polycystin-2 / 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: 9009.580 Da / Num. of mol.: 1 / Fragment: UNP residues 720-797
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 / Details: protein x
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-1H NOESY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HN(CO)CA
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11223D 1H-15N NOESY
11323D 1H-15N TOCSY
11413D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] protein, 5 % D2O, 0.05 % sodium azide, 10 uM PMSF, 2 mM TRIS pH7.4, 150 mM sodium chloride, 20 mM Ca2+, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-15N] protein, 2 mM TRIS pH7.4, 20 mM Ca2+, 150 mM sodium chloride, 5% D2O, 10 uM PMSF, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-13C; U-15N]1
5 %D2O1
0.05 %sodium azide1
10 uMPMSF1
2 mMTRIS pH7.41
150 mMsodium chloride1
20 mMCa2+1
1 mMprotein[U-15N]2
2 mMTRIS pH7.42
20 mMCa2+2
150 mMsodium chloride2
5 %D2O2
10 uMPMSF2
Sample conditionsIonic strength: 0.150 / pH: 7.4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
SparkyGoddardpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
PSVSBhattacharya and Montelionegeometry optimization
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: XPLOR-NIH / Software ordinal: 1
NMR constraintsNOE constraints total: 506 / NOE intraresidue total count: 103 / NOE long range total count: 41 / NOE medium range total count: 194 / NOE sequential total count: 168
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.9 ° / Maximum upper distance constraint violation: 0.44 Å
NMR ensemble rmsDistance rms dev: 0.06 Å

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