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- PDB-6a70: Structure of the human PKD1/PKD2 complex -

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Basic information

Entry
Database: PDB / ID: 6a70
TitleStructure of the human PKD1/PKD2 complex
Components
  • Polycystin-1
  • Polycystin-2
KeywordsMEMBRANE PROTEIN / Asymmetric complex / polycystic kidney disease
Function / homology
Function and homology information


metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / 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 distal tubule morphogenesis / nitrogen cycle metabolic process / 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 / lung epithelium development / metanephric ascending thin limb development / lymph vessel morphogenesis / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / mitocytosis / metanephric proximal tubule development / HLH domain binding / calcium-induced calcium release activity / calcium-independent cell-matrix adhesion / Wnt receptor activity / cilium organization / genitalia development / migrasome / VxPx cargo-targeting to cilium / detection of mechanical stimulus / muscle alpha-actinin binding / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / cellular response to hydrostatic pressure / Golgi-associated vesicle membrane / response to fluid shear stress / cellular response to fluid shear stress / metanephric collecting duct development / cation channel complex / outward rectifier potassium channel activity / non-motile cilium / cartilage development / actinin binding / cellular response to osmotic stress / determination of left/right symmetry / digestive tract development / : / voltage-gated monoatomic cation channel activity / neural tube development / voltage-gated sodium channel activity / aorta development / motile cilium / ciliary membrane / branching involved in ureteric bud morphogenesis / cartilage condensation / skin development / protein heterotetramerization / branching morphogenesis of an epithelial tube / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / establishment of cell polarity / homophilic cell-cell adhesion / centrosome duplication / regulation of G1/S transition of mitotic cell cycle / lateral plasma membrane / anatomical structure morphogenesis / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / embryonic placenta development / regulation of cell adhesion / monoatomic cation channel activity / voltage-gated calcium channel activity / transcription regulator inhibitor activity / cytoskeletal protein binding / regulation of proteasomal protein catabolic process / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / calcium channel complex / sodium ion transmembrane transport / cellular response to calcium ion / protein export from nucleus / basal plasma membrane / cytoplasmic vesicle membrane / regulation of mitotic spindle organization / cellular response to cAMP / cell-matrix adhesion / cellular response to reactive oxygen species / lumenal side of endoplasmic reticulum membrane / protein tetramerization / kidney development / phosphoprotein binding / establishment of localization in cell / liver development / peptidyl-serine phosphorylation
Similarity search - Function
Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. ...Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / PKD domain / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Polycystic kidney disease (PKD) domain profile. / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / PKD domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Voltage-dependent channel domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin-like fold
Similarity search - Domain/homology
Polycystin-1 / Polycystin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSu, Q. / Hu, F. / Ge, X. / Lei, J. / Yu, S. / Wang, T. / Zhou, Q. / Mei, C. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31630017 China
CitationJournal: Science / Year: 2018
Title: Structure of the human PKD1-PKD2 complex.
Authors: Qiang Su / Feizhuo Hu / Xiaofei Ge / Jianlin Lei / Shengqiang Yu / Tingliang Wang / Qiang Zhou / Changlin Mei / Yigong Shi /
Abstract: Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron ...Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron microscopy structure of truncated human PKD1-PKD2 complex assembled in a 1:3 ratio. PKD1 contains a voltage-gated ion channel (VGIC) fold that interacts with PKD2 to form the domain-swapped, yet noncanonical, transient receptor potential (TRP) channel architecture. The S6 helix in PKD1 is broken in the middle, with the extracellular half, S6a, resembling pore helix 1 in a typical TRP channel. Three positively charged, cavity-facing residues on S6b may block cation permeation. In addition to the VGIC, a five-transmembrane helix domain and a cytosolic PLAT domain were resolved in PKD1. The PKD1-PKD2 complex structure establishes a framework for dissecting the function and disease mechanisms of the PKD proteins.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4Feb 26, 2020Group: Source and taxonomy / Category: em_entity_assembly_recombinant / entity_src_gen
Item: _em_entity_assembly_recombinant.cell / _em_entity_assembly_recombinant.ncbi_tax_id ..._em_entity_assembly_recombinant.cell / _em_entity_assembly_recombinant.ncbi_tax_id / _em_entity_assembly_recombinant.organism / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.5Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Polycystin-2
B: Polycystin-1
F: Polycystin-2
G: Polycystin-2


Theoretical massNumber of molelcules
Total (without water)326,8954
Polymers326,8954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19530 Å2
ΔGint-174 kcal/mol
Surface area108390 Å2

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Components

#1: Protein Polycystin-2 / PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 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: 66623.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13563
#2: Protein Polycystin-1 / PC1 / Autosomal dominant polycystic kidney disease 1 protein


Mass: 127024.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD1 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P98161

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: the structure of an asymmetric complex / Type: COMPLEX
Details: Samples were obtained by co-expression in 293F cells. A complex contains one PKD1 subunit and three PKD2 subunits.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.31 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: HOMO SAPIENS (human) / Cell: HEK293F
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMHEPES 7.5HEPES1
30.06 %digitonindigitonin1
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27296 / Symmetry type: POINT

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