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- PDB-7a6u: Cryo-EM structure of the cytoplasmic domain of human TRPC6 -

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Basic information

Entry
Database: PDB / ID: 7a6u
TitleCryo-EM structure of the cytoplasmic domain of human TRPC6
ComponentsShort transient receptor potential channel 6
KeywordsMEMBRANE PROTEIN / Ion transport protein Transient receptor ion channel II / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of ion transmembrane transporter activity / slit diaphragm / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / cation channel complex ...positive regulation of ion transmembrane transporter activity / slit diaphragm / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / cation channel complex / actinin binding / clathrin binding / TRP channels / monoatomic cation transport / regulation of cytosolic calcium ion concentration / single fertilization / monoatomic cation channel activity / positive regulation of neuron differentiation / calcium ion transmembrane transport / calcium channel activity / cellular response to hydrogen peroxide / neuron differentiation / positive regulation of cytosolic calcium ion concentration / ATPase binding / actin binding / cellular response to hypoxia / protein homodimerization activity / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transient receptor potential channel, canonical 6 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...Transient receptor potential channel, canonical 6 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Short transient receptor potential channel 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsGrieben, M. / Pike, A.C.W. / Wang, D. / Mukhopadhyay, S.M.M. / Chalk, R. / Marsden, B.D. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Grieben, M. / Pike, A.C.W. / Wang, D. / Mukhopadhyay, S.M.M. / Chalk, R. / Marsden, B.D. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Cryo-EM structure of the cytoplasmic domain of human TRPC6
Authors: Grieben, M. / Carpenter, E.P.
History
DepositionAug 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp / em_software / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _em_software.name / _em_software.version / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Short transient receptor potential channel 6
B: Short transient receptor potential channel 6
C: Short transient receptor potential channel 6
D: Short transient receptor potential channel 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,4008
Polymers439,1394
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16960 Å2
ΔGint-88 kcal/mol
Surface area59690 Å2
MethodPISA

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Components

#1: Protein
Short transient receptor potential channel 6 / TrpC6 / Transient receptor protein 6 / TRP-6


Mass: 109784.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC6, TRP6 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y210
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically
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: Short transient receptor potential channel 6 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental 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
120 mMHEPES1
2200 mMPotassium chlorideKCl1
30.33 % (w/v)Trehalose1
41 mMTCEP1
5Amphipol A8-351
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample remained stable and monodispersed in the amphipol A8-35.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278.15 K
Details: 2.5 microlitres were applied to the grid and blotted for 4secs prior to plunge in liquid 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 / Nominal magnification: 165000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1198
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC2.15.0CTF correction
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC2.15.03D reconstruction
13PHENIXmodel refinement
CTF correctionDetails: Patch CTF routine in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28365 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5YX9

5yx9


Accession code: 5YX9 / Source name: PDB / Type: experimental model

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