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- EMDB-3523: cryoEM Structure of Polycystin-2 in complex with cations and lipids -

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Basic information

Entry
Database: EMDB / ID: 3523
TitlecryoEM Structure of Polycystin-2 in complex with cations and lipids
Map data
SamplePolycystin-2Polycystin 2:
(ligand) x 5
Function / homologyPolycystic kidney disease type 2 protein / EF-hand domain pair / Polycystin cation channel, PKD1/PKD2 / Voltage-dependent channel domain superfamily / Polycystin cation channel / VxPx cargo-targeting to cilium / EF-hand calcium-binding domain profile. / EF-hand domain / cellular response to hydrostatic pressure / metanephric smooth muscle tissue development ...Polycystic kidney disease type 2 protein / EF-hand domain pair / Polycystin cation channel, PKD1/PKD2 / Voltage-dependent channel domain superfamily / Polycystin cation channel / VxPx cargo-targeting to cilium / EF-hand calcium-binding domain profile. / EF-hand domain / cellular response to hydrostatic pressure / metanephric smooth muscle tissue development / metanephric cortex development / metanephric distal tubule development / detection of nodal flow / metanephric cortical collecting duct development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric ascending thin limb development / metanephric part of ureteric bud development / determination of liver left/right asymmetry / integral component of cytoplasmic side of endoplasmic reticulum membrane / renal tubule morphogenesis / calcium-induced calcium release activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / basal cortex / renal artery morphogenesis / outward rectifier potassium channel activity / non-motile cilium / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / cellular response to osmotic stress / HLH domain binding / voltage-gated sodium channel activity / placenta blood vessel development / go:0030814: / regulation of calcium ion import / detection of mechanical stimulus / motile cilium / aorta development / cytoplasmic sequestering of transcription factor / sodium ion transmembrane transport / ciliary membrane / voltage-gated cation channel activity / actinin binding / voltage-gated ion channel activity / neural tube development / determination of left/right symmetry / negative regulation of G1/S transition of mitotic cell cycle / JAK-STAT cascade / potassium channel activity / ciliary basal body / spinal cord development / potassium ion transmembrane transport / basal plasma membrane / branching involved in ureteric bud morphogenesis / voltage-gated calcium channel activity / heart looping / release of sequestered calcium ion into cytosol / voltage-gated potassium channel activity / cytoskeletal protein binding / negative regulation of ryanodine-sensitive calcium-release channel activity / embryonic placenta development / calcium ion transmembrane transport / positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle / centrosome duplication / cilium / calcium ion transport / mitotic spindle / cellular response to calcium ion / positive regulation of cell cycle arrest / cellular response to cAMP / liver development / cellular response to reactive oxygen species / cytoplasmic vesicle membrane / phosphoprotein binding / cellular response to fluid shear stress / integral component of lumenal side of endoplasmic reticulum membrane / cell-cell junction / cell cycle arrest / ATPase binding / lamellipodium / ion channel binding / protein homotetramerization / heart development / positive regulation of nitric oxide biosynthetic process / regulation of cell proliferation / negative regulation of cell proliferation / endoplasmic reticulum membrane / signaling receptor binding / calcium ion binding / endoplasmic reticulum / integral component of plasma membrane / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / Polycystin-2
Function and homology information
Sourcehomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsWilkes M / Madej MG
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Molecular insights into lipid-assisted Ca regulation of the TRP channel Polycystin-2.
Authors: Martin Wilkes / M Gregor Madej / Lydia Kreuter / Daniel Rhinow / Veronika Heinz / Silvia De Sanctis / Sabine Ruppel / Rebecca M Richter / Friederike Joos / Marina Grieben / Ashley C W Pike / Juha T Huiskonen / Elisabeth P Carpenter / Werner Kühlbrandt / Ralph Witzgall / Christine Ziegler
Validation ReportPDB-ID: 5mke

SummaryFull reportAbout validation report
DateDeposition: Dec 4, 2016 / Header (metadata) release: Dec 28, 2016 / Map release: Jan 18, 2017 / Last update: Feb 15, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0345
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0345
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5mke
  • Surface level: 0.0345
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3523.map.gz (map file in CCP4 format, 18967 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
1.14 Å/pix.
= 191.52 Å
168 pix
1.14 Å/pix.
= 191.52 Å
168 pix
1.14 Å/pix.
= 191.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density
Contour Level:0.0345 (by author), 0.0345 (movie #1):
Minimum - Maximum-0.06904477 - 0.09819269
Average (Standard dev.)0.001177011 (0.0061609545)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin000
Limit167167167
Spacing168168168
CellA=B=C: 191.52 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z191.520191.520191.520
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0690.0980.001

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Supplemental data

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Sample components

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Entire Polycystin-2

EntireName: Polycystin-2 / Number of components: 7

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Component #1: protein, Polycystin-2

ProteinName: Polycystin-2Polycystin 2 / Recombinant expression: No
SourceSpecies: homo sapiens (human)
Source (engineered)Expression System: homo sapiens (human)

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Component #2: protein, Polycystin-2

ProteinName: Polycystin-2Polycystin 2 / Recombinant expression: No
MassTheoretical: 109.820086 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #4: ligand, 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID

LigandName: 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.215289 kDa

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Component #5: ligand, 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

LigandName: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.647883 kDa

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Component #6: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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Component #7: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 4.1 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 42268
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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