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- PDB-5z1w: Cryo-EM structure of polycystic kidney disease-like channel PKD2L1 -

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Basic information

Entry
Database: PDB / ID: 5z1w
TitleCryo-EM structure of polycystic kidney disease-like channel PKD2L1
ComponentsPolycystic kidney disease 2-like 1 protein
KeywordsMEMBRANE PROTEIN / channel / cryo-EM
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 / cellular response to pH / cation channel complex / muscle alpha-actinin binding / cellular response to acidic pH / non-motile cilium / inorganic cation transmembrane transport ...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 / cellular response to pH / cation channel complex / muscle alpha-actinin binding / 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 / protein tetramerization / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / protein homotetramerization / transmembrane transporter binding / receptor complex / calcium ion binding / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsZhang, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1.
Authors: Qiang Su / Feizhuo Hu / Yuxia Liu / Xiaofei Ge / Changlin Mei / Shengqiang Yu / Aiwen Shen / Qiang Zhou / Chuangye Yan / Jianlin Lei / Yanqing Zhang / Xiaodong Liu / Tingliang Wang /
Abstract: PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel ...PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel that can be regulated by voltage, protons, and calcium. Despite its considerable importance, the molecular mechanisms underlying PKD2L1 regulations are largely unknown. Here, we determine the PKD2L1 atomic structure at 3.38 Å resolution by cryo-electron microscopy, whereby side chains of nearly all residues are assigned. Unlike its ortholog PKD2, the pore helix (PH) and transmembrane segment 6 (S6) of PKD2L1, which are involved in upper and lower-gate opening, adopt an open conformation. Structural comparisons of PKD2L1 with a PKD2-based homologous model indicate that the pore domain dilation is coupled to conformational changes of voltage-sensing domains (VSDs) via a series of π-π interactions, suggesting a potential PKD2L1 gating mechanism.
History
DepositionDec 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
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Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)265,05816
Polymers262,4044
Non-polymers2,65412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23740 Å2
ΔGint-140 kcal/mol
Surface area78150 Å2

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Components

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


Mass: 65600.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkd2l1, Trpp3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A2A259
#2: 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.: 12
Source method: isolated from a genetically manipulated source
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
Has protein modificationY

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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: PKD2L1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 / Cs: 0.001 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22296 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01114232
ELECTRON MICROSCOPYf_angle_d0.8919428
ELECTRON MICROSCOPYf_dihedral_angle_d10.02610736
ELECTRON MICROSCOPYf_chiral_restr0.0562192
ELECTRON MICROSCOPYf_plane_restr0.0062428

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