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- EMDB-7786: human PKD2 F604P mutant -

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Basic information

Entry
Database: EMDB / ID: 7786
Titlehuman PKD2 F604P mutant
Map dataHuman PKD2 F604P mutant
SamplePKD2Polycystin 2:
Polycystin-2Polycystin 2 / ligand
Function / homologyEF-hand calcium-binding domain profile. / Polycystic kidney disease type 2 protein / Polycystin cation channel, PKD1/PKD2 / Voltage-dependent channel domain superfamily / Polycystin cation channel / EF-hand domain / EF-hand domain pair / VxPx cargo-targeting to cilium / metanephric cortical collecting duct development / metanephric distal tubule development ...EF-hand calcium-binding domain profile. / Polycystic kidney disease type 2 protein / Polycystin cation channel, PKD1/PKD2 / Voltage-dependent channel domain superfamily / Polycystin cation channel / EF-hand domain / EF-hand domain pair / VxPx cargo-targeting to cilium / metanephric cortical collecting duct development / metanephric distal tubule development / cellular response to hydrostatic pressure / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / mesonephric duct development / polycystin complex / mesonephric tubule 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 / go:0030814: / renal tubule morphogenesis / calcium-induced calcium release activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / renal artery morphogenesis / basal cortex / outward rectifier potassium channel activity / non-motile cilium / metanephric S-shaped body morphogenesis / metanephric mesenchyme development / cellular response to osmotic stress / HLH domain binding / placenta blood vessel development / voltage-gated sodium channel activity / regulation of calcium ion import / detection of mechanical stimulus / aorta development / cytoplasmic sequestering of transcription factor / sodium ion transmembrane transport / motile cilium / voltage-gated cation channel activity / actinin binding / voltage-gated ion channel activity / neural tube development / ciliary membrane / 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 / voltage-gated calcium channel activity / branching involved in ureteric bud morphogenesis / heart looping / release of sequestered calcium ion into cytosol / voltage-gated potassium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / embryonic placenta development / positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle / calcium ion transmembrane transport / centrosome duplication / cilium / calcium ion transport / mitotic spindle / cytoskeletal protein binding / 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 / lamellipodium / ATPase binding / protein homotetramerization / heart development / ion channel binding / 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 / 3.54 Å resolution
AuthorsZheng W / Yang X / Bulkley D / Chen XZ / Cao E
CitationJournal: Nat Commun / Year: 2018
Title: Hydrophobic pore gates regulate ion permeation in polycystic kidney disease 2 and 2L1 channels.
Authors: Wang Zheng / Xiaoyong Yang / Ruikun Hu / Ruiqi Cai / Laura Hofmann / Zhifei Wang / Qiaolin Hu / Xiong Liu / David Bulkey / Yong Yu / Jingfeng Tang / Veit Flockerzi / Ying Cao / Erhu Cao / Xing-Zhen Chen
Validation ReportPDB-ID: 6d1w

SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2018 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6d1w
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7786.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.22 Å/pix.
= 233.395 Å
192 pix
1.22 Å/pix.
= 233.395 Å
192 pix
1.22 Å/pix.
= 233.395 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.12531123 - 0.21940334
Average (Standard dev.)0.0012095302 (0.008277643)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.0.0.
Limit191.191.191.
Spacing192192192
CellA=B=C: 233.3952 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21559895833331.21559895833331.2155989583333
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z233.395233.395233.395
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1250.2190.001

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Supplemental data

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Sample components

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Entire PKD2

EntireName: PKD2 / Number of components: 3

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Component #1: cellular-component, PKD2

Cellular-componentName: PKD2Polycystin 2 / Recombinant expression: No
MassTheoretical: 300 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293S

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Component #2: protein, Polycystin-2

ProteinName: Polycystin-2Polycystin 2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 84.996336 kDa
SourceSpecies: Homo sapiens (human)
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: 12 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 387454
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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