[English] 日本語
Yorodumi
- SASDFC5: Enhanced disease susceptibility 1 (EDS1) (Enhanced disease suscep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFC5
SampleEnhanced disease susceptibility 1 (EDS1)
  • Enhanced disease susceptibility (protein), EDS1, Arabidopsis thaliana
Function / homology
Function and homology information


aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to singlet oxygen / lipase activity / regulation of hydrogen peroxide metabolic process / chloroplast ...aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to singlet oxygen / lipase activity / regulation of hydrogen peroxide metabolic process / chloroplast / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / nucleus / cytoplasm / cytosol
Similarity search - Function
EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Contact author
  • Martin Voss (University of cologne)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2806
Type: dummy / Radius of dummy atoms: 2.60 A / Chi-square value: 0.824 / P-value: 0.059642
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Enhanced disease susceptibility 1 (EDS1) / Specimen concentration: 5 mg/ml
BufferName: 50 mM NaCl, 50 mM HEPES, 1% glyercol, 1 mM DTT / pH: 8
Entity #1480Name: EDS1 / Type: protein / Description: Enhanced disease susceptibility / Formula weight: 71.689 / Num. of mol.: 1 / Source: Arabidopsis thaliana / References: UniProt: Q9SU72
Sequence: MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAFL KNLEAIIDPR TSFQASVEMA VRSRKQIVFT GHSSGGATAI LATVWYLEKY FIRNPNVYLE PRCVTFGAPL VGDSIFSHAL ...Sequence:
MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAFL KNLEAIIDPR TSFQASVEMA VRSRKQIVFT GHSSGGATAI LATVWYLEKY FIRNPNVYLE PRCVTFGAPL VGDSIFSHAL GREKWSRFFV NFVSRFDIVP RIMLARKASV EETLPHVLAQ LDPRKSSVQE SEQRITEFYT RVMRDTSTVA NQAVCELTGS AEAFLETLSS FLELSPYRPA GTFVFSTEKR LVAVNNSDAI LQMLFYTSQA SDEQEWSLIP FRSIRDHHSY EELVQSMGKK LFNHLDGENS IESTLNDLGV STRGRQYVQA ALEEEKKRVE NQKKIIQVIE QERFLKKLAW IEDEYKPKCQ AHKNGYYDSF KVSNEENDFK ANVKRAELAG VFDEVLGLMK KCQLPDEFEG DIDWIKLATR YRRLVEPLDI ANYHRHLKNE DTGPYMKRGR PTRYIYAQRG YEHYILKPNG MIAEDVFWNK VNGLNLGLQL EEIQETLKNS GSECGSCFWA EVEELKGKPY EEVEVRVKTL EGMLGEWITD GEVDDKEIFL EGSTFRKWWI TLPKNHKSHS PLRDYMMDEI TDT

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.867 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Enhanced disease susceptibility 1 (EDS1) / Measurement date: May 19, 2015 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 2 sec. / Number of frames: 1495 / Unit: 1/nm /
MinMax
Q0.0364 4.9389
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 512 /
MinMax
Q0.229265 2.6335
P(R) point1 512
R0 10.53
Result
Type of curve: sec
Comments: The data were re-binned to calculate the p(r) profile and corresponding model fit.
ExperimentalPorod
MW72 kDa58 kDa
Volume-92 nm3

P(R)GuinierGuinier error
Forward scattering, I0152.6 151.87 0.47
Radius of gyration, Rg3.08 nm3.09 nm0.02

MinMax
D-10.53
Guinier point23 80

+
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://pdbjlvh1.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