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- PDB-6du8: Human Polycsytin 2-l1 -

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Basic information

Entry
Database: PDB / ID: 6du8
TitleHuman Polycsytin 2-l1
ComponentsPolycystic kidney disease 2-like 1 protein
KeywordsMEMBRANE PROTEIN / polycystic 2-l1 / pc2l1 / pkd2l1 / TRPP2
Function / homology
Function and homology information


sour taste receptor activity / detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / pH-gated monoatomic ion channel activity / response to water / osmolarity-sensing monoatomic cation channel activity / calcium-activated potassium channel activity / detection of mechanical stimulus / muscle alpha-actinin binding ...sour taste receptor activity / detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / pH-gated monoatomic ion channel activity / response to water / osmolarity-sensing monoatomic cation channel activity / calcium-activated potassium channel activity / detection of mechanical stimulus / muscle alpha-actinin binding / calcium-activated cation channel activity / cellular response to acidic pH / non-motile cilium / : / ciliary membrane / smoothened signaling pathway / sodium channel activity / monoatomic cation transmembrane transport / alpha-actinin binding / monoatomic cation transport / monoatomic cation channel activity / cytoskeletal protein binding / potassium ion transmembrane transport / calcium channel complex / sodium ion transmembrane transport / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / protein homotetramerization / transmembrane transporter binding / receptor complex / intracellular membrane-bounded organelle / calcium ion binding / cell surface / endoplasmic reticulum / identical protein binding / membrane / 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
Similarity search - Domain/homology
Polycystin-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsHulse, R.E. / Clapham, D.E. / Li, Z. / Huang, R.K. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of the polycystin 2-l1 ion channel.
Authors: Raymond E Hulse / Zongli Li / Rick K Huang / Jin Zhang / David E Clapham /
Abstract: We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation- ...We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3Jul 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 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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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)369,1678
Polymers368,2834
Non-polymers8854
Water00
1


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

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Components

#1: Protein
Polycystic kidney disease 2-like 1 protein / Polycystin-2 homolog / Polycystin-2L1 / Polycystin-L / Polycystin-L1


Mass: 92070.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2L1, PKD2L, PKDL, TRPP3 / Plasmid: pEG / Cell (production host): HEK-293S GnTl / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9P0L9
#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.: 4
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: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human polycystic 2-l / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Homotetrameric assembly of polycystic 2-l1 / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.547 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pEG
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium ChlorideKCL1
250 mMHEPESC8H18N2O4S1
350 mMSodium ChlorideNaCl1
41 mMCalcium ChlorideCaCl21
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: polycystic 2-l1 stabilized in amphipol PMAL-C8
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 60 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
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119334 / Num. of class averages: 8 / Symmetry type: POINT

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