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- EMDB-11674: Cryo-EM structure of the cytoplasmic domain of human TRPC6 -

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Basic information

Entry
Database: EMDB / ID: EMD-11674
TitleCryo-EM structure of the cytoplasmic domain of human TRPC6
Map datasharpened map at 3.62A, 0.822A pix
Sample
  • Organelle or cellular component: Short transient receptor potential channel 6
    • Protein or peptide: Short transient receptor potential channel 6
  • Ligand: UNKNOWN ATOM OR ION
Function / homology
Function and homology information


positive regulation of ion transmembrane transporter activity / slit diaphragm / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / cation channel complex / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / TRP channels ...positive regulation of ion transmembrane transporter activity / slit diaphragm / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / cation channel complex / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / TRP channels / single fertilization / monoatomic cation transport / monoatomic cation channel activity / regulation of cytosolic calcium ion concentration / calcium ion transmembrane transport / calcium channel activity / positive regulation of cytosolic calcium ion concentration / protein homodimerization activity / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transient receptor potential channel, canonical 6 / Transient receptor ion channel II / Transient receptor ion channel domain / 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 II / Transient receptor ion channel domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsGrieben M / Pike ACW / Wang D / Mukhopadhyay SMM / Chalk R / Marsden BD / Burgess-Brown NA / Arrowsmith CH / Edwards AM / Bountra C ...Grieben M / Pike ACW / Wang D / Mukhopadhyay SMM / Chalk R / Marsden BD / Burgess-Brown NA / Arrowsmith CH / Edwards AM / Bountra C / Carpenter EP / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2 items
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 EP
History
DepositionAug 26, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a6u
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11674.png

Downloads & links

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Map

FileDownload / File: emd_11674.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map at 3.62A, 0.822A pix
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.0721 / Movie #1: 0.1
Minimum - Maximum-0.27850828 - 0.45640033
Average (Standard dev.)0.0013726286 (±0.022954756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 205.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z205.500205.500205.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.2790.4560.001

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Supplemental data

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Mask #1

Fileemd_11674_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A, 3.62A, 0.822A pix

Fileemd_11674_half_map_1.map
Annotationhalf map A, 3.62A, 0.822A pix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B, 3.62A, 0.822A pix

Fileemd_11674_half_map_2.map
Annotationhalf map B, 3.62A, 0.822A pix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Short transient receptor potential channel 6

EntireName: Short transient receptor potential channel 6
Components
  • Organelle or cellular component: Short transient receptor potential channel 6
    • Protein or peptide: Short transient receptor potential channel 6
  • Ligand: UNKNOWN ATOM OR ION

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Supramolecule #1: Short transient receptor potential channel 6

SupramoleculeName: Short transient receptor potential channel 6 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #1: Short transient receptor potential channel 6

MacromoleculeName: Short transient receptor potential channel 6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.784695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQSPAFGPR RGSSPRGAAG AAARRNESQD YLLMDSELGE DGCPQAPLPC YGYYPCFRGS DNRLAHRRQT VLREKGRRLA NRGPAYMFS DRSTSLSIEE ERFLDAAEYG NIPVVRKMLE ECHSLNVNCV DYMGQNALQL AVANEHLEIT ELLLKKENLS R VGDALLLA ...String:
MSQSPAFGPR RGSSPRGAAG AAARRNESQD YLLMDSELGE DGCPQAPLPC YGYYPCFRGS DNRLAHRRQT VLREKGRRLA NRGPAYMFS DRSTSLSIEE ERFLDAAEYG NIPVVRKMLE ECHSLNVNCV DYMGQNALQL AVANEHLEIT ELLLKKENLS R VGDALLLA ISKGYVRIVE AILSHPAFAE GKRLATSPSQ SELQQDDFYA YDEDGTRFSH DVTPIILAAH CQEYEIVHTL LR KGARIER PHDYFCKCND CNQKQKHDSF SHSRSRINAY KGLASPAYLS LSSEDPVMTA LELSNELAVL ANIEKEFKND YKK LSMQCK DFVVGLLDLC RNTEEVEAIL NGDVETLQSG DHGRPNLSRL KLAIKYEVKK FVAHPNCQQQ LLSIWYENLS GLRQ QTMAV KFLVVLAVAI GLPFLALIYW FAPCSKMGKI MRGPFMKFVA HAASFTIFLG LLVMNAADRF EGTKLLPNET STDNA KQLF RMKTSCFSWM EMLIISWVIG MIWAECKEIW TQGPKEYLFE LWNMLDFGML AIFAASFIAR FMAFWHASKA QSIIDA NDT LKDLTKVTLG DNVKYYNLAR IKWDPSDPQI ISEGLYAIAV VLSFSRIAYI LPANESFGPL QISLGRTVKD IFKFMVI FI MVFVAFMIGM FNLYSYYIGA KQNEAFTTVE ESFKTLFWAI FGLSEVKSVV INYNHKFIEN IGYVLYGVYN VTMVIVLL N MLIAMINSSF QEIEDDADVE WKFARAKLWF SYFEEGRTLP VPFNLVPSPK SLFYLLLKLK KWISELFQGH KKGFQEDAE MNKINEEKKL GILGSHEDLS KLSLDKKQVG HNKQPSIRSS EDFHLNSFNN PPRQYQKIMK RLIKRYVLQA QIDKESDEVN EGELKEIKQ DISSLRYELL EEKSQNTEDL AELIRELGEK LSMEPNQEET NRAENLYFQS HHHHHHHHHH DYKDDDDK

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Macromolecule #2: UNKNOWN ATOM OR ION

MacromoleculeName: UNKNOWN ATOM OR ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: UNX
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
200.0 mMPotassium chlorideKCl
0.33 % (w/v)Trehalose
1.0 mMTCEP
Amphipol A8-35
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV
Details: 2.5 microlitres were applied to the grid and blotted for 4secs prior to plunge in liquid ethane.
DetailsThis sample remained stable and monodispersed in the amphipol A8-35.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number grids imaged: 1 / Number real images: 1198 / Average electron dose: 53.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.15.0) / Details: Patch CTF routine in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 28365
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5yx9

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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