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- PDB-7d7f: Structure of PKD1L3-CTD/PKD2L1 in calcium-bound state -

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Basic information

Entry
Database: PDB / ID: 7d7f
TitleStructure of PKD1L3-CTD/PKD2L1 in calcium-bound state
Components
  • Polycystic kidney disease 2-like 1 protein
  • Polycystic kidney disease protein 1-like 3
KeywordsTRANSPORT PROTEIN / Heterotetrameric TRP channel / Calcium / Primary cilia / PKD
Function / homology
Function and homology information


detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / response to water / calcium-activated potassium channel activity / detection of mechanical stimulus / cellular response to pH / muscle alpha-actinin binding / cation channel complex / cellular response to acidic pH / non-motile cilium ...detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / response to water / calcium-activated potassium channel activity / detection of mechanical stimulus / cellular response to pH / muscle alpha-actinin binding / cation channel complex / cellular response to acidic pH / non-motile cilium / inorganic cation transmembrane transport / sodium channel activity / ciliary membrane / smoothened signaling pathway / monoatomic cation transport / monoatomic cation channel activity / calcium channel complex / potassium ion transmembrane transport / protein tetramerization / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / carbohydrate binding / protein homotetramerization / transmembrane transporter binding / receptor complex / calcium ion binding / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Polycystin-1 like, PLAT/LH2 domain / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / GAIN domain superfamily / GPCR proteolysis site, GPS, motif ...Polycystin-1 like, PLAT/LH2 domain / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / C-type lectin-like/link domain superfamily / C-type lectin fold / Voltage-dependent channel domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Polycystin-2-like protein 1 / Polycystin-1-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSu, Q. / Shi, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for Ca activation of the heteromeric PKD1L3/PKD2L1 channel.
Authors: Qiang Su / Mengying Chen / Yan Wang / Bin Li / Dan Jing / Xiechao Zhan / Yong Yu / Yigong Shi /
Abstract: The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization ...The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization of heterotetrametric TRP-like channels. Here we show that a truncated PKD1L3/PKD2L1 complex with the C-terminal TRP-fold fragment of PKD1L3 retains both Ca and acid-induced channel activities. Cryo-EM structures of this core heterocomplex with or without supplemented Ca were determined at resolutions of 3.1 Å and 3.4 Å, respectively. The heterotetramer, with a pseudo-symmetric TRP architecture of 1:3 stoichiometry, has an asymmetric selectivity filter (SF) guarded by Lys2069 from PKD1L3 and Asp523 from the three PKD2L1 subunits. Ca-entrance to the SF vestibule is accompanied by a swing motion of Lys2069 on PKD1L3. The S6 of PKD1L3 is pushed inward by the S4-S5 linker of the nearby PKD2L1 (PKD2L1-III), resulting in an elongated intracellular gate which seals the pore domain. Comparison of the apo and Ca-loaded complexes unveils an unprecedented Ca binding site in the extracellular cleft of the voltage-sensing domain (VSD) of PKD2L1-III, but not the other three VSDs. Structure-guided mutagenic studies support this unconventional site to be responsible for Ca-induced channel activation through an allosteric mechanism.
History
DepositionOct 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
B: Polycystic kidney disease 2-like 1 protein
C: Polycystic kidney disease 2-like 1 protein
D: Polycystic kidney disease 2-like 1 protein
A: Polycystic kidney disease protein 1-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,65919
Polymers270,2464
Non-polymers2,41215
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Polycystic kidney disease 2-like 1 protein / Polycystin-2 homolog


Mass: 69234.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkd2l1, Trpp3 / Production host: Homo sapiens (human) / References: UniProt: A2A259
#2: Protein Polycystic kidney disease protein 1-like 3 / PC1-like 3 protein / Polycystin-1L3


Mass: 62541.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkd1l3, 71B10 / Production host: Homo sapiens (human) / References: UniProt: Q2EG98
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 10 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: 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: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149903 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00815888
ELECTRON MICROSCOPYf_angle_d0.74121601
ELECTRON MICROSCOPYf_dihedral_angle_d23.2112124
ELECTRON MICROSCOPYf_chiral_restr0.0522428
ELECTRON MICROSCOPYf_plane_restr0.0052681

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