[English] 日本語
- PDB-6e1p: Structure of AtTPC1(DDE) in state 2 -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6e1p
TitleStructure of AtTPC1(DDE) in state 2
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 / 3.7 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

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8960
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


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)173,39823

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#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: D230N, D444N, Q518E / 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

Mass: 40.078 Da / Num. of mol.: 5 / Formula: Ca / Calcium
#3: Chemical

Mass: 256.424 Da / Num. of mol.: 16 / Formula: C16H32O2 / Palmitic acid
#4: Water ChemComp-HOH / water

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

Experimental details


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


EM software
2SerialEMimage acquisition
4GctfCTF correction
5RELIONCTF correction
10PHENIX1.13-2998model refinement
11RELION2.1.0initial Euler assignment
12RELION2.1.0final Euler assignment
14RELION2.1.03D reconstruction
Particle selectionNumber of particles selected: 996035
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 67308 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
RefineStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011911047
ELECTRON MICROSCOPYf_angle_d1.205214912
ELECTRON MICROSCOPYf_chiral_restr0.06451670
ELECTRON MICROSCOPYf_plane_restr0.00781814
ELECTRON MICROSCOPYf_dihedral_angle_d10.25206240

About Yorodumi


Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

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

Read more


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