[English] 日本語
Yorodumi
- SASDCY6: T2 in b-DDM micelle (SEC-SAXS) (Mechanosensitive channel T2, T2 +... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDCY6
SampleT2 in b-DDM micelle (SEC-SAXS)
  • Mechanosensitive channel T2 (protein), T2, Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)
  • n-Dodecyl-β-D-Maltopyranoside (other), b-DDM, Synthetic compound
Function / homologyMechanosensitive ion channel MscS, archaea/bacteria type / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / mechanosensitive monoatomic ion channel activity / LSM domain superfamily / membrane / Mechanosensitive ion channel MscS domain-containing protein
Function and homology information
Biological speciesThermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) (archaea)
Synthetic compound (others)
CitationDate: 2018 Feb
Title: Saposin Lipid Nanoparticles: A Highly Versatile and Modular Tool for Membrane Protein Research
Authors: Flayhan A / Mertens H / Ural-Blimke Y / Martinez Molledo M / Svergun D
Contact author
  • Haydyn Mertens (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1498
Type: dummy / Software: (2.9.0) / Radius of dummy atoms: 3.50 A / Symmetry: P7 / Chi-square value: 3.360
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: T2 in b-DDM micelle (SEC-SAXS) / Entity id: 786 / 789
BufferName: 20 mM Tris 150 mM NaCl 5 % glycerol 0.03 % DDM / pH: 7.5
Entity #786Name: T2 / Type: protein / Description: Mechanosensitive channel T2 / Formula weight: 32.887 / Num. of mol.: 7
Source: Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)
References: UniProt: Q97AH5
Sequence: MDRAKGKSIA VYVGSMIVLI IVLLALLYVL SLFHIVPIKF SRILYAVVIG LVIYAIVRIV TKYVERFISL HSEFKHLKYI VFIISLLGYF IISLAVLAAL GIDVSSVILG SAFLSAIIGL AAQSVLANVF GGLFLSIVRP FKLGDHIVVN TWQFPVSFPS YPPKYFSRDF ...Sequence:
MDRAKGKSIA VYVGSMIVLI IVLLALLYVL SLFHIVPIKF SRILYAVVIG LVIYAIVRIV TKYVERFISL HSEFKHLKYI VFIISLLGYF IISLAVLAAL GIDVSSVILG SAFLSAIIGL AAQSVLANVF GGLFLSIVRP FKLGDHIVVN TWQFPVSFPS YPPKYFSRDF IEGSIYRGIV SDISINYTSI ALESGDVVKI PNNIMIQAAI TLRHGSVTVQ ARYEVPKYIN FNDIYNKIVD EVGTLPGARN IGVMIDETTV NTYIILVRGD FQGEDADLVR SQILQKVIGI VEPLKKQ
Entity #789Name: b-DDM / Type: other / Description: n-Dodecyl-β-D-Maltopyranoside / Formula weight: 0.511 / Source: Synthetic compound

-
Experimental information

BeamInstrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
DetectorName: Pilatus 2M
Scan
Title: T2_DDM / Measurement date: May 29, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 3600 / Unit: 1/nm /
MinMax
Q0.0778 4.607
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1000 /
MinMax
Q0.0778114 2.80185
P(R) point1 1000
R0 16.5
Result
Type of curve: single_conc
ExperimentalExperimental errorPorodPorod error
MW355 kDa40 560 kDa60
Volume--896 nm390

P(R)P(R) errorGuinierGuinier error
Forward scattering, I0250 5 251 5
Radius of gyration, Rg5.6 nm0.2 5.6 nm0.1

MinMaxError
D-16.5 0.5
Guinier point1 30 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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