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- PDB-6d1w: human PKD2 F604P mutant -

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Entry
Database: PDB / ID: 6d1w
Titlehuman PKD2 F604P mutant
ComponentsPolycystin-2Polycystin 2
KeywordsTRANSPORT PROTEIN / Ion Channel / TRP channel / PKD2 / PC2 / TRPP2
Function / homologyPolycystin cation channel, PKD1/PKD2 / VxPx cargo-targeting to cilium / EF-hand calcium-binding domain profile. / EF-hand domain / Polycystin cation channel / Polycystic kidney disease type 2 protein / Voltage-dependent channel domain superfamily / EF-hand domain pair / metanephric smooth muscle tissue development / metanephric cortex development ...Polycystin cation channel, PKD1/PKD2 / VxPx cargo-targeting to cilium / EF-hand calcium-binding domain profile. / EF-hand domain / Polycystin cation channel / Polycystic kidney disease type 2 protein / Voltage-dependent channel domain superfamily / EF-hand domain pair / metanephric smooth muscle tissue development / metanephric cortex development / cellular response to hydrostatic pressure / metanephric cortical collecting duct development / detection of nodal flow / metanephric distal tubule development / cell-cell signaling by wnt / mesonephric tubule development / mesonephric duct development / polycystin complex / metanephric ascending thin limb development / determination of liver left/right asymmetry / metanephric part of ureteric bud development / 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 / inorganic cation transmembrane transport / renal artery morphogenesis / cation channel complex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / non-motile cilium / HLH domain binding / outward rectifier potassium channel activity / cellular response to osmotic stress / placenta blood vessel development / regulation of calcium ion import / voltage-gated sodium channel activity / detection of mechanical stimulus / cytoplasmic sequestering of transcription factor / aorta development / sodium ion transmembrane transport / motile cilium / voltage-gated ion channel activity / determination of left/right symmetry / actinin binding / ciliary membrane / cation channel activity / voltage-gated cation channel activity / muscle alpha-actinin binding / ciliary basal body / receptor signaling pathway via JAK-STAT / neural tube development / negative regulation of G1/S transition of mitotic cell cycle / potassium channel activity / spinal cord development / potassium ion transmembrane transport / branching involved in ureteric bud morphogenesis / heart looping / voltage-gated calcium channel activity / voltage-gated potassium channel activity / release of sequestered calcium ion into cytosol / negative regulation of ryanodine-sensitive calcium-release channel activity / embryonic placenta development / centrosome duplication / calcium channel activity / calcium ion transmembrane transport / basal plasma membrane / cilium / calcium ion transport / cellular response to calcium ion / positive regulation of cell cycle arrest / cytoskeletal protein binding / mitotic spindle / cellular response to cAMP / cellular response to reactive oxygen species / cytoplasmic vesicle membrane / phosphoprotein binding / liver development / cellular response to fluid shear stress / integral component of lumenal side of endoplasmic reticulum membrane / protein heterotetramerization / cell-cell junction / cell cycle arrest / protein tetramerization / regulation of cell population proliferation / lamellipodium / protein homotetramerization / ATPase binding / heart development / positive regulation of nitric oxide biosynthetic process / ion channel binding / negative regulation of cell population proliferation / endoplasmic reticulum membrane / signaling receptor binding / calcium ion binding / endoplasmic reticulum / integral component of plasma membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.54 Å resolution
AuthorsZheng, W. / Yang, X. / Bulkley, D. / Chen, X.Z. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2018 / Release: Jun 27, 2018

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Assembly

Deposited unit
A: Polycystin-2
B: Polycystin-2
C: Polycystin-2
D: Polycystin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,64016
Polyers339,9854
Non-polymers2,65412
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26210
ΔGint (kcal/M)-175
Surface area (Å2)81220
MethodPISA

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Components

#1: Protein/peptide
Polycystin-2 / Polycystin 2 / PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 protein / Polycystwin / R48321 / Transient receptor potential cation channel subfamily P member 2


Mass: 84996.336 Da / Num. of mol.: 4 / Mutation: F604P / Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2Polycystin 2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q13563
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 12 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PKD2Polycystin 2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 300 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Cell: HEK293S / Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 387454 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00814892
ELECTRON MICROSCOPYf_angle_d0.75420304
ELECTRON MICROSCOPYf_dihedral_angle_d11.80611388
ELECTRON MICROSCOPYf_chiral_restr0.0422368
ELECTRON MICROSCOPYf_plane_restr0.0042496

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