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- EMDB-46979: PKD2 ion channel, R638C variant -

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Basic information

Entry
Database: EMDB / ID: EMD-46979
TitlePKD2 ion channel, R638C variant
Map data
Sample
  • Complex: PKD2 R638C variant protomer
    • Protein or peptide: Polycystin-2
KeywordsIon channel / 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 / HLH domain binding / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / calcium-induced calcium release activity / cilium organization / migrasome / VxPx cargo-targeting to cilium / detection of mechanical stimulus / cation channel complex / muscle alpha-actinin binding / 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 / outward rectifier potassium channel activity / actinin binding / cellular response to osmotic stress / non-motile cilium / voltage-gated monoatomic cation channel activity / determination of left/right symmetry / inorganic cation transmembrane transport / aorta development / neural tube development / motile cilium / voltage-gated sodium channel activity / ciliary membrane / branching involved in ureteric bud morphogenesis / protein heterotetramerization / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / transcription regulator inhibitor activity / cytoplasmic side of endoplasmic reticulum membrane / heart looping / centrosome duplication / voltage-gated potassium channel activity / potassium channel activity / embryonic placenta development / cell surface receptor signaling pathway via JAK-STAT / voltage-gated calcium channel activity / monoatomic cation channel activity / cytoskeletal protein binding / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / cytoplasmic vesicle membrane / sodium ion transmembrane transport / cellular response to calcium ion / liver development / ciliary basal body / basal plasma membrane / cellular response to reactive oxygen species / establishment of localization in cell / phosphoprotein binding / lumenal side of endoplasmic reticulum membrane / protein tetramerization / cilium / Wnt signaling pathway / calcium ion transmembrane transport / mitotic spindle / intracellular calcium ion homeostasis / 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 / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / 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: 2.7 Å
AuthorsEsarte Palomero O / DeCaen PG
Funding support United States, 4 items
OrganizationGrant numberCountry
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)R01 DK131118-01 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
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Tristan Ian Croll /
Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
History
DepositionSep 11, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46979.png

Downloads & links

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Map

FileDownload / File: emd_46979.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.32 Å/pix.
x 864 pix.
= 279.504 Å		0.32 Å/pix.
x 864 pix.
= 279.504 Å		0.32 Å/pix.
x 864 pix.
= 279.504 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3235 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.029
Minimum - Maximum-0.19798936 - 0.24279253
Average (Standard dev.)0.000014733541 (±0.006302597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions864864864
Spacing864864864
CellA=B=C: 279.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46979_msk_1.map
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Additional map: Unsharpened map

Fileemd_46979_additional_1.map
AnnotationUnsharpened map
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Half map: #1

Fileemd_46979_half_map_1.map
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Half map: #2

Fileemd_46979_half_map_2.map
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Sample components

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Entire : PKD2 R638C variant protomer

EntireName: PKD2 R638C variant protomer
Components
  • Complex: PKD2 R638C variant protomer
    • Protein or peptide: Polycystin-2

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Supramolecule #1: PKD2 R638C variant protomer

SupramoleculeName: PKD2 R638C variant protomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.95 kDa/nm

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Macromolecule #1: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 1 / Details: PKD2 (52-793), R638C variant / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.049383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GEIEMQRIRQ AAARDPPAGA AASPSPPLSS CSRQAWSRDN PGFEAEEEEE EVEGEEGGMV VEMDVEWRPG SRRSAASSAV SSVGARSRG LGGYHGAGHP SGRRRRREDQ GPPCPSPVGG GDPLHRHLPL EGQPPRVAWA ERLVRGLRGL WGTRLMEESS T NREKYLKS ...String:
GEIEMQRIRQ AAARDPPAGA AASPSPPLSS CSRQAWSRDN PGFEAEEEEE EVEGEEGGMV VEMDVEWRPG SRRSAASSAV SSVGARSRG LGGYHGAGHP SGRRRRREDQ GPPCPSPVGG GDPLHRHLPL EGQPPRVAWA ERLVRGLRGL WGTRLMEESS T NREKYLKS VLRELVTYLL FLIVLCILTY GMMSSNVYYY TRMMSQLFLD TPVSKTEKTN FKTLSSMEDF WKFTEGSLLD GL YWKMQPS NQTEADNRSF IFYENLLLGV PRIRQLRVRN GSCSIPQDLR DEIKECYDVY SVSSEDRAPF GPRNGTAWIY TSE KDLNGS SHWGIIATYS GAGYYLDLSR TREETAAQVA SLKKNVWLDR GTRATFIDFS VYNANINLFC VVRLLVEFPA TGGV IPSWQ FQPLKLIRYV TTFDFFLAAC EIIFCFFIFY YVVEEILEIR IHKLHYFRSF WNCLDVVIVV LSVVAIGINI YRTSN VEVL LQFLEDQNTF PNFEHLAYWQ IQFNNIAAVT VFFVWIKLFK FINFNRTMSQ LSTTMSRCAK DLFGFAIMFF IIFLAY AQL AYLVFGTQVD DFSTFQECIF TQFCIILGDI NFAEIEEANR VLGPIYFTTF VFFMFFILLN MFLAIINDTY SEVKSDL AQ QKAEMELSDL IRKGYHKALV KLKLKKNTVD DISESLRQGG GKLNFDELRQ DLKGKGHTDA EIEAIFTKYD QDGDQELT E HEHQQMRDDL EKEREDLDLD

UniProtKB: Polycystin-2

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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
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
DetailsStabilized in amphipol A8-35. Monodisperse sample after gel filtration in Superdex 200

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Electron microscopy

MicroscopeFEI TITAN 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: 50 / Average electron dose: 60.0 e/Å2
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: 2084635
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio 3D
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 665417
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 50 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Overall B value: 113.1
Output model

PDB-9dli:
PKD2 ion channel, R638C variant

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