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- PDB-9dwt: PKD2 ion channel, F634A mutant -

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Basic information

Entry
Database: PDB / ID: 9dwt
TitlePKD2 ion channel, F634A mutant
ComponentsPolycystin-2
KeywordsMEMBRANE PROTEIN / Ion channel / TRP channel / polycystin
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 / renal tubule morphogenesis ...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 / renal tubule morphogenesis / determination of liver left/right asymmetry / metanephric ascending thin limb development / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / HLH domain binding / calcium-induced calcium release activity / cilium organization / VxPx cargo-targeting to cilium / migrasome / muscle alpha-actinin binding / detection of mechanical stimulus / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / cellular response to hydrostatic pressure / cellular response to fluid shear stress / cation channel complex / outward rectifier potassium channel activity / non-motile cilium / cellular response to osmotic stress / actinin binding / determination of left/right symmetry / : / voltage-gated monoatomic cation channel activity / neural tube development / voltage-gated sodium channel activity / aorta development / motile cilium / branching involved in ureteric bud morphogenesis / ciliary membrane / protein heterotetramerization / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / centrosome duplication / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / embryonic placenta development / voltage-gated calcium channel activity / monoatomic cation channel activity / transcription regulator inhibitor activity / cytoskeletal protein binding / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / cellular response to calcium ion / basal plasma membrane / sodium ion transmembrane transport / cellular response to cAMP / cytoplasmic vesicle membrane / cellular response to reactive oxygen species / protein tetramerization / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / establishment of localization in cell / liver development / calcium ion transmembrane transport / Wnt signaling pathway / intracellular calcium ion homeostasis / positive regulation of nitric oxide biosynthetic process / cell-cell junction / mitotic spindle / calcium ion transport / lamellipodium / regulation of cell population proliferation / heart development / ATPase binding / protein homotetramerization / basolateral plasma membrane / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / cilium / ciliary basal body / signaling receptor binding / negative regulation of cell population proliferation / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / membrane
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 calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsEsarte Palomero, O. / DeCaen, P.G.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK131118-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK123463-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)(F32DK137477-01A1 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)TL1DK132769 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)U2CDK129917 United States
CitationJournal: To Be Published
Title: PKD2 ion channel, F629S variant
Authors: Esarte Palomero, O. / DeCaen, P.G.
History
DepositionOct 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycystin-2
B: Polycystin-2
C: Polycystin-2
D: Polycystin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,1945
Polymers224,1534
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Polycystin-2 / PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 ...PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 protein / Polycystwin / R48321 / Transient receptor potential cation channel subfamily P member 2


Mass: 56038.363 Da / Num. of mol.: 4 / Mutation: F634A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2 / Plasmid: pCMV / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): expi293 / References: UniProt: Q13563
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PKD2 ion channel F634A mutant protomer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.3396 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293 / Cell: expi293 / Plasmid: pCMV
Buffer solutionpH: 7.4
Details: 25 mM HEPES-NaOH, 150 mM NaCl, 1 mM CaCl2, 1 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
225 mM(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)HEPES1
31 mMCalcium ChlorideCaCl21
41 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Stabilized in amphipol A8-35. Monodisperse sample after gel filtration in a Superdex 200 column.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K
Details: Vitrification carried in air. Ethane temperature -183 C

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14969 / Details: 50 frame movie stacks. Super-resolution mode
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2SerialEMv4.1.0betaimage acquisition
4cryoSPARC4.5CTF correction
7UCSF ChimeraX1.8model fitting
8ISOLDE1.8model fitting
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
12cryoSPARCclassification
13cryoSPARC4.53D reconstruction
14ISOLDE1.8model refinement
15PHENIX1.21.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1441572 / Details: Micrographs were blob picked (130-170 angstrom)
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98122 / Algorithm: FOURIER SPACE
Details: Final reconstruction was generated using C4 symmetry
Symmetry type: POINT
Atomic model buildingB value: 101 / Space: REAL
Details: The initial Alphafold model was fitted to the map using ChimeraX. Refinement was performed using ISOLDE and PHENIX.
Atomic model buildingChain residue range: 180-925 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415592
ELECTRON MICROSCOPYf_angle_d0.44521156
ELECTRON MICROSCOPYf_dihedral_angle_d4.6112021
ELECTRON MICROSCOPYf_chiral_restr0.0372372
ELECTRON MICROSCOPYf_plane_restr0.0032628

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