[English] 日本語
Yorodumi
- PDB-6e1m: Structure of AtTPC1(DDE) reconstituted in saposin A -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6e1m
TitleStructure of AtTPC1(DDE) reconstituted in saposin A
ComponentsTwo pore calcium channel protein 1
KeywordsMEMBRANE PROTEIN / Two-pore channel / membrane protein
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
Specimen sourceArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsKintzer, A.F. / Green, E.M. / Cheng, Y. / Stroud, R.M.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2018 / Release: Sep 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 19, 2018Structure modelrepositoryInitial release
1.1Oct 3, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8957
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Two pore calcium channel protein 1
B: Two pore calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,37525
Polyers169,0942
Non-polymers5,28023
Water362
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein/peptide Two pore calcium channel protein 1 / Calcium channel protein 1 / AtCCH1 / Fatty acid oxygenation up-regulated protein 2 / Voltage-dependent calcium channel protein TPC1 / AtTPC1


Mass: 84547.203 Da / Num. of mol.: 2 / Mutation: N240D, N454D, Q528E / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPC1, CCH1, FOU2, At4g03560, F9H3.19, T5L23.5 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q94KI8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Formula: Ca / Calcium
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 14 / Formula: C16H32O2 / Palmitic acid
#4: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 2 / Formula: C39H77O8P / Phosphatidic acid
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: AtTPC1(DDE) / Type: COMPLEX / Entity ID: 1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.3
SpecimenConc.: 0.8 mg/ml / Details: Sample reconstituted into saposin A. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 20 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 / Calibrated magnification: 41132 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 2 / Number of real images: 3408
Image scansMovie frames/image: 60 / Used frames/image: 2-60

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
5RELIONCTF correction
10PHENIX1.13-2998model refinement
11RELION2.1.0initial Euler assignment
12RELION2.1.0final Euler assignment
14RELION2.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 996035
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 224577 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more