[English] 日本語
Yorodumi
- PDB-6drk: Structure of TRPM2 ion channel receptor by single particle electr... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6drk
TitleStructure of TRPM2 ion channel receptor by single particle electron cryo-microscopy, Apo state
ComponentsTransient receptor potential cation channel, subfamily M, member 2
KeywordsTRANSPORT PROTEIN
Function / homologyun:a0a0r4in04:
Function and homology information
Specimen sourceDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsDu, J. / Lu, W. / Huang, Y. / Winkler, P. / Sun, W.
CitationJournal: Nature / Year: 2018
Title: Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium.
Authors: Yihe Huang / Paige A Winkler / Weinan Sun / Wei Lü / Juan Du
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 12, 2018 / Release: Sep 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 19, 2018Structure modelrepositoryInitial release
1.1Sep 26, 2018Structure modelData collection / Structure summarystruct_struct.title
1.2Oct 10, 2018Structure modelData collection / Database references / Structure summarycitation / entity_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8901
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transient receptor potential cation channel, subfamily M, member 2
C: Transient receptor potential cation channel, subfamily M, member 2
B: Transient receptor potential cation channel, subfamily M, member 2
D: Transient receptor potential cation channel, subfamily M, member 2


Theoretical massNumber of molelcules
Total (without water)674,0504
Polyers674,0504
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)16950
ΔGint (kcal/M)-174
Surface area (Å2)262010

-
Components

#1: Protein/peptide
Transient receptor potential cation channel, subfamily M, member 2


Mass: 168512.578 Da / Num. of mol.: 4 / Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trpm2 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A0R4IN04

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ion channel 1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: YES
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Mammalia (mammals)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: dev_3084: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 183041 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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 EBI / 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

-
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