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- EMDB-47264: PKD2 ion channel, F634A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-47264
TitlePKD2 ion channel, F634A mutant
Map dataPKD2 mutant F634A sharpened EM map
Sample
  • Complex: PKD2 ion channel F634A mutant protomer
    • Protein or peptide: Polycystin-2
  • Ligand: CALCIUM ION
KeywordsIon channel / TRP channel / polycystin / membrane protein
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 / VxPx cargo-targeting to cilium / cilium organization / migrasome / muscle alpha-actinin binding / detection of mechanical stimulus / regulation of calcium ion import / calcium-induced calcium release activity / voltage-gated monoatomic ion channel activity / placenta blood vessel development / cellular response to hydrostatic pressure / cation channel complex / cellular response to fluid shear stress / outward rectifier potassium channel activity / cellular response to osmotic stress / non-motile cilium / motile cilium / actinin binding / determination of left/right symmetry / : / neural tube development / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / aorta development / branching involved in ureteric bud morphogenesis / ciliary membrane / negative regulation of G1/S transition of mitotic cell cycle / protein heterotetramerization / spinal cord development / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / heart looping / centrosome duplication / voltage-gated potassium channel activity / embryonic placenta development / potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / voltage-gated calcium channel activity / transcription regulator inhibitor activity / monoatomic cation channel activity / cytoskeletal protein binding / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / cellular response to calcium ion / establishment of localization in cell / cellular response to cAMP / cytoplasmic vesicle membrane / basal plasma membrane / sodium ion transmembrane transport / cellular response to reactive oxygen species / lumenal side of endoplasmic reticulum membrane / protein tetramerization / liver development / phosphoprotein binding / 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 / regulation of cell population proliferation / lamellipodium / 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 / negative regulation of cell population proliferation / signaling receptor binding / 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 / membrane / identical protein binding
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsEsarte Palomero O / DeCaen PG
Funding support United States, 5 items
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 PG
History
DepositionOct 10, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47264.png

Downloads & links

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Map

FileDownload / File: emd_47264.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPKD2 mutant F634A sharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 259.52 Å		0.65 Å/pix.
x 400 pix.
= 259.52 Å		0.65 Å/pix.
x 400 pix.
= 259.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6488 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.071
Minimum - Maximum-0.2961952 - 0.4370261
Average (Standard dev.)0.0003364614 (±0.015294541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 259.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47264_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: PKD2 mutant F634A unsharpened EM map

Fileemd_47264_additional_1.map
AnnotationPKD2 mutant F634A unsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PKD2 mutant F634A EM Half map A

Fileemd_47264_half_map_1.map
AnnotationPKD2 mutant F634A EM Half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PKD2 mutant F634A EM Half map B

Fileemd_47264_half_map_2.map
AnnotationPKD2 mutant F634A EM Half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PKD2 ion channel F634A mutant protomer

EntireName: PKD2 ion channel F634A mutant protomer
Components
  • Complex: PKD2 ion channel F634A mutant protomer
    • Protein or peptide: Polycystin-2
  • Ligand: CALCIUM ION

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Supramolecule #1: PKD2 ion channel F634A mutant protomer

SupramoleculeName: PKD2 ion channel F634A mutant protomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 339.6 KDa

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Macromolecule #1: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.038363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EKYLKSVLRE LVTYLLFLIV LCILTYGMMS SNVYYYTRMM SQLFLDTPVS KTEKTNFKTL SSMEDFWKFT EGSLLDGLYW KMQPSNQTE ADNRSFIFYE NLLLGVPRIR QLRVRNGSCS IPQDLRDEIK ECYDVYSVSS EDRAPFGPRN GTAWIYTSEK D LNGSSHWG ...String:
EKYLKSVLRE LVTYLLFLIV LCILTYGMMS SNVYYYTRMM SQLFLDTPVS KTEKTNFKTL SSMEDFWKFT EGSLLDGLYW KMQPSNQTE ADNRSFIFYE NLLLGVPRIR QLRVRNGSCS IPQDLRDEIK ECYDVYSVSS EDRAPFGPRN GTAWIYTSEK D LNGSSHWG IIATYSGAGY YLDLSRTREE TAAQVASLKK NVWLDRGTRA TFIDFSVYNA NINLFCVVRL LVEFPATGGV IP SWQFQPL KLIRYVTTFD FFLAACEIIF CFFIFYYVVE EILEIRIHKL HYFRSFWNCL DVVIVVLSVV AIGINIYRTS NVE VLLQFL EDQNTFPNFE HLAYWQIQFN NIAAVTVFFV WIKLFKFINF NRTMSQLSTT MSRCAKDLFG FAIMFFIIFL AYAQ LAYLV FGTQVDDFST FQECIATQFR IILGDINFAE IEEANRVLGP IYFTTFVFFM FFILLNMFLA IINDTYSEVK SDLAQ

UniProtKB: Polycystin-2

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
25.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
1.0 mMCaCl2Calcium Chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine

Details: 25 mM HEPES-NaOH, 150 mM NaCl, 1 mM CaCl2, 1 mM TCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA EM GP
Details: Vitrification carried in air. Ethane temperature -183 C.
DetailsStabilized in amphipol A8-35. Monodisperse sample after gel filtration in a Superdex 200 column.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 14969 / Average electron dose: 60.0 e/Å2 / Details: 50 frame movie stacks. Super-resolution mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1441572 / Details: Micrographs were blob picked (130-170 angstrom)
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5)
Details: Final reconstruction was generated using C4 symmetry
Number images used: 98122
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Residue range: 180-925 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsThe initial Alphafold model was fitted to the map using ChimeraX. Refinement was performed using ISOLDE and PHENIX.
RefinementSpace: REAL / Overall B value: 101
Output model

PDB-9dwt:
PKD2 ion channel, F634A mutant

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