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- PDB-6d1w: human PKD2 F604P mutant -

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Basic information

Entry
Database: PDB / ID: 6d1w
Titlehuman PKD2 F604P mutant
ComponentsPolycystin-2Polycystin 2
KeywordsTRANSPORT PROTEIN / Ion Channel / TRP channel / PKD2 / PC2 / TRPP2
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
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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