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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-2Polycystin 2
KeywordsMEMBRANE PROTEIN / Asymmetric complex / polycystic kidney disease
Function / homologyLeucine-rich repeat domain superfamily / Polycystic kidney disease type 1 protein / PKD/REJ-like domain / EF-hand domain / Leucine-rich repeat / C-type lectin-like / PLAT/LH2 domain / PKD domain / Cysteine-rich flanking region, C-terminal / C-type lectin domain profile. ...Leucine-rich repeat domain superfamily / Polycystic kidney disease type 1 protein / PKD/REJ-like domain / EF-hand domain / Leucine-rich repeat / C-type lectin-like / PLAT/LH2 domain / PKD domain / Cysteine-rich flanking region, C-terminal / C-type lectin domain profile. / Leucine-rich repeat N-terminal domain / Leucine-rich repeat, typical subtype / Leucine rich repeat / Polycystin cation channel / GPS motif / REJ domain / PLAT/LH2 domain / PKD domain / PKD domain superfamily / Lectin C-type domain / PLAT/LH2 domain superfamily / Carbohydrate-binding WSC / WSC domain / Polycystic kidney disease (PKD) domain profile. / C-type lectin-like/link domain superfamily / C-type lectin fold / REJ domain / PKD/Chitinase domain / VxPx cargo-targeting to cilium / Polycystin cation channel, PKD1/PKD2 / EF-hand domain pair / Polycystin cation channel / Polycystic kidney disease type 2 protein / Voltage-dependent channel domain superfamily / Leucine-rich repeat profile. / WSC domain profile. / REJ domain profile. / EF-hand calcium-binding domain profile. / PLAT domain profile. / GPS domain profile. / Immunoglobulin-like fold / metanephric proximal tubule development / metanephric distal tubule morphogenesis / metanephric collecting duct development / metanephric smooth muscle tissue development / metanephric cortical collecting duct development / metanephric distal tubule development / detection of nodal flow / metanephric cortex development / cellular response to hydrostatic pressure / mesonephric tubule development / mesonephric duct development / polycystin complex / go:0030814: / metanephric part of ureteric bud development / metanephric ascending thin limb development / determination of liver left/right asymmetry / integral component of cytoplasmic side of endoplasmic reticulum membrane / lung epithelium development / 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 / lymph vessel morphogenesis / outward rectifier potassium channel activity / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / non-motile cilium / cellular response to osmotic stress / genitalia development / HLH domain binding / calcium-independent cell-matrix adhesion / Golgi-associated vesicle membrane / placenta blood vessel development / voltage-gated sodium channel activity / regulation of calcium ion import / response to fluid shear stress / detection of mechanical stimulus / motile cilium / sodium ion transmembrane transport / cytoplasmic sequestering of transcription factor / voltage-gated cation channel activity / aorta development / actinin binding / voltage-gated ion channel activity / neural tube development / muscle alpha-actinin binding / ciliary membrane / determination of left/right symmetry / negative regulation of G1/S transition of mitotic cell cycle / digestive tract development / regulation of mitotic spindle organization / JAK-STAT cascade / protein export from nucleus / skin development / potassium channel activity / cartilage development / spinal cord development / potassium ion transmembrane transport
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsSu, Q. / Hu, F. / Ge, X. / Lei, J. / Yu, S. / Wang, T. / Zhou, Q. / Mei, C. / Shi, Y.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 29, 2018 / Release: Aug 15, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 15, 2018Structure modelrepositoryInitial release
1.1Aug 29, 2018Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
1.2Sep 19, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.title

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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
Polyers326,8954
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)19530
ΔGint (kcal/M)-174
Surface area (Å2)108390

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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: 66623.406 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2Polycystin 2 / Cell line (production host): 293F cells / Production host: Mammalian expression vector pCK9 (others) / References: UniProt: Q13563
#2: Protein/peptide Polycystin-1 / / PC1 / Autosomal dominant polycystic kidney disease 1 protein


Mass: 127024.836 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PKD1 / Cell line (production host): 293F cells / Production host: Mammalian expression vector pCK9 (others) / References: UniProt: P98161

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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: 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: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 0.31 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Cell: 293F cells / Organism: Mammalian expression vector pCK9 (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMsodium chlorideNaCl1
220 mMHEPES 7.5HEPES1
30.06 %digitonindigitonin1
SpecimenConc.: 10 mg/ml / Details: This sample was monodisperse. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Number of particles: 27296 / Symmetry type: POINT

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