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- EMDB-25825: AtTPC1 D454N-EDTA state II -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25825
TitleAtTPC1 D454N-EDTA state II
Map datalocally sharpened map using Deepemhancer
Sample
  • Complex: AtTPC1 D454N-EDTA state II
    • Protein or peptide: Two pore calcium channel protein 1
Function / homology
Function and homology information


regulation of jasmonic acid biosynthetic process / seed germination / regulation of stomatal movement / plant-type vacuole / vacuole / vacuolar membrane / monoatomic ion channel complex / voltage-gated calcium channel activity / calcium-mediated signaling / calcium ion transport ...regulation of jasmonic acid biosynthetic process / seed germination / regulation of stomatal movement / plant-type vacuole / vacuole / vacuolar membrane / monoatomic ion channel complex / voltage-gated calcium channel activity / calcium-mediated signaling / calcium ion transport / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Two pore calcium channel protein 1, plant / Voltage-dependent channel domain superfamily / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Two pore calcium channel protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDickinson MS / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Molecular basis of multistep voltage activation in plant two-pore channel 1.
Authors: Miles Sasha Dickinson / Jinping Lu / Meghna Gupta / Irene Marten / Rainer Hedrich / Robert M Stroud /
Abstract: Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels ...Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.
History
DepositionDec 30, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25825.png

Downloads & links

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Map

FileDownload / File: emd_25825.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocally sharpened map using Deepemhancer
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.104
Minimum - Maximum-0.06785761 - 2.1746447
Average (Standard dev.)0.0005196666 (±0.015795533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 360.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_25825_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_25825_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_25825_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtTPC1 D454N-EDTA state II

EntireName: AtTPC1 D454N-EDTA state II
Components
  • Complex: AtTPC1 D454N-EDTA state II
    • Protein or peptide: Two pore calcium channel protein 1

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Supramolecule #1: AtTPC1 D454N-EDTA state II

SupramoleculeName: AtTPC1 D454N-EDTA state II / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 168 KDa

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Macromolecule #1: Two pore calcium channel protein 1

MacromoleculeName: Two pore calcium channel protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.589844 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: TDRVRRSEAI THGTPFQKAA ALVDLAEDGI GLPVEILDQS SFGESARYYF IFTRLDLIWS LNYFALLFLN FFEQPLWCEK NPKPSCKDR DYYYLGELPY LTNAESIIYE VITLAILLVH TFFPISYEGS RIFWTSRLNL VKVACVVILF VDVLVDFLYL S PLAFDFLP ...String:
TDRVRRSEAI THGTPFQKAA ALVDLAEDGI GLPVEILDQS SFGESARYYF IFTRLDLIWS LNYFALLFLN FFEQPLWCEK NPKPSCKDR DYYYLGELPY LTNAESIIYE VITLAILLVH TFFPISYEGS RIFWTSRLNL VKVACVVILF VDVLVDFLYL S PLAFDFLP FRIAPYVRVI IFILSIRELR DTLVLLSGML GTYLNILALW MLFLLFASWI AFVMFEDTQQ GLTVFTSYGA TL YQMFILF TTSNNPDVWI PAYKSSRWSS VFFVLYVLIG VYFVTNLILA VVYDSFKEQL AKQVSGMDQM KRRMLEKAFG LID SDKNGE IDKNQCIKLF EQLTNYRTLP KISKEEFGLI FDELDDTRDF KINKDEFADL CQAIALRFQK EEVPSLFEHF PQIY HSALS QQLRAFVRSP NFGYAISFIL IINFIAVVVE TTLNIEESSA QKPWQVAEFV FGWIYVLEMA LKIYTYGFEN YWREG ANRF DFLVTWVIVI GETATFITPD ENTFFSNGEW IRYLLLARML RLIRLLMNVQ RYRAFIATFI TLIPSLMPYL GTIFCV LCI YCSIGVQVFG GLVNAGNKKL FETELAEDDY LLFNFNDYPN GMVTLFNLLV MGNWQVWMES YKDLTGTWWS ITYFVSF YV ITILLLLNLV VAFVLEAFFT ELDLEEEEKC QGQ

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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

Concentration5 mg/mL
BufferpH: 7.5
Details: 50 mM Tris, 200 mM NaCl and 0.06% glycodiosgenin, 1 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

25798

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68456

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7tdd:
AtTPC1 D454N-EDTA state II

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