[English] 日本語
Yorodumi
- EMDB-47260: PKD2 ion channel, F629S variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47260
TitlePKD2 ion channel, F629S variant
Map dataEM Map PKD2 Variant F629S
Sample
  • Complex: PKD2 ion channel F629S variant 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 / 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: 2.76 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 9, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47260.png

Downloads & links

-
Map

FileDownload / File: emd_47260.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM Map PKD2 Variant F629S
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: 0.102
Minimum - Maximum-0.44219112 - 0.5949078
Average (Standard dev.)0.00036152132 (±0.020962054)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_47260_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM Half Map A PKD2 Variant F629S

Fileemd_47260_half_map_1.map
AnnotationEM Half Map A PKD2 Variant F629S
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM Half Map B PKD2 Variant F629S

Fileemd_47260_half_map_2.map
AnnotationEM Half Map B PKD2 Variant F629S
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PKD2 ion channel F629S variant protomer

EntireName: PKD2 ion channel F629S variant protomer
Components
  • Complex: PKD2 ion channel F629S variant protomer
    • Protein or peptide: Polycystin-2
  • Ligand: CALCIUM ION

-
Supramolecule #1: PKD2 ion channel F629S variant protomer

SupramoleculeName: PKD2 ion channel F629S variant protomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 339.6 KDa

-
Macromolecule #1: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 1
Details: PKD2 variant F629S (residues 52-793) was expressed with an N-terminal StrepII-MBP-TEV cleaved prior to macromolecular analysis
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.043344 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 DFSTSQECIF TQFRIILGDI NFAEIEEANR VLGPIYFTTF VFFMFFILLN MFLAIINDTY SEVKSDL AQ QKAEMELSDL IRKGYHKALV KLKLKKNTVD DISESLRQGG GKLNFDELRQ DLKGKGHTDA EIEAIFTKYD QDGDQELT E HEHQQMRDDL EKEREDLDLD

UniProtKB: Polycystin-2

-
Macromolecule #2: CALCIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 / Details: 15 mA
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.

-
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: 9145 / 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

+
Image processing

Particle selectionNumber selected: 1046126
Details: Denoised micrographs were blob picked (130-170 angstrom)
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5)
Details: Final reconstruction performed with C4 symmetry imposed
Number images used: 215875
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)

-
Atomic model buiding 1

Initial modelChain - 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: 107.9
Output model

PDB-9dwq:
PKD2 ion channel, F629S variant

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more