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- EMDB-8956: Structure of AtTPC1(DDE) reconstituted in saposin A with cat06 Fab -

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Basic information

Entry
Database: EMDB / ID: 8956
TitleStructure of AtTPC1(DDE) reconstituted in saposin A with cat06 Fab
Map data
SampleAtTPC1(DDE) reconstituted in saposin A:
Two pore calcium channel protein 1 / cat06 light chain / cat06 heavy chain / (ligand) x 3
Function / homologyEF-hand domain / Stimuli-sensing channels / EF-hand calcium-binding domain profile. / Ion transport protein / Two pore calcium channel protein 1 / Voltage-dependent channel domain superfamily / EF-hand domain pair / Ion transport domain / regulation of jasmonic acid biosynthetic process / plant-type vacuole ...EF-hand domain / Stimuli-sensing channels / EF-hand calcium-binding domain profile. / Ion transport protein / Two pore calcium channel protein 1 / Voltage-dependent channel domain superfamily / EF-hand domain pair / Ion transport domain / regulation of jasmonic acid biosynthetic process / plant-type vacuole / seed germination / regulation of stomatal movement / vacuolar membrane / vacuole / voltage-gated calcium channel activity / regulation of ion transmembrane transport / calcium ion transport / calcium-mediated signaling / calcium ion binding / Golgi apparatus / integral component of membrane / identical protein binding / plasma membrane / Two pore calcium channel protein 1
Function and homology information
SourceArabidopsis thaliana (thale cress) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsGreen EM / Kintzer AF / Stroud RM / Cheng Y
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for activation of voltage sensor domains in an ion channel TPC1.
Authors: Alexander F Kintzer / Evan M Green / Pawel K Dominik / Michael Bridges / Jean-Paul Armache / Dawid Deneka / Sangwoo S Kim / Wayne Hubbell / Anthony A Kossiakoff / Yifan Cheng / Robert M Stroud
Validation ReportPDB-ID: 6e1k

SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2018 / Header (metadata) release: Sep 19, 2018 / Map release: Sep 19, 2018 / Last update: Oct 3, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6e1k
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8956.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.22 Å/pix.
= 311.194 Å
256 pix
1.22 Å/pix.
= 311.194 Å
256 pix
1.22 Å/pix.
= 311.194 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density
Contour Level:6.0 (by author), 6 (movie #1):
Minimum - Maximum-55.498252999999998 - 58.423157000000003
Average (Standard dev.)-0.000000013179107 (1.0000005)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 311.1936 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21560156251.21560156251.2156015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z311.194311.194311.194
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-55.49858.423-0.000

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Supplemental data

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Sample components

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Entire AtTPC1(DDE) reconstituted in saposin A

EntireName: AtTPC1(DDE) reconstituted in saposin A / Number of components: 7

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Component #1: protein, AtTPC1(DDE) reconstituted in saposin A

ProteinName: AtTPC1(DDE) reconstituted in saposin A / Recombinant expression: No
SourceSpecies: Arabidopsis thaliana (thale cress)

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Component #2: protein, Two pore calcium channel protein 1

ProteinName: Two pore calcium channel protein 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 84.547203 kDa
SourceSpecies: Arabidopsis thaliana (thale cress)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, cat06 light chain

ProteinName: cat06 light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.171703 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, cat06 heavy chain

ProteinName: cat06 heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.786658 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Component #6: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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Component #7: ligand, water

LigandName: water / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.8 mg/ml / pH: 7.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 20 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000.0 X (nominal), 41132.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3408

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 224577
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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