[English] 日本語
Yorodumi
- SASDGE2: Human mitochondrial iron-sulfur cluster assembly ISCA2 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGE2
SampleHuman mitochondrial iron-sulfur cluster assembly ISCA2 protein
  • Iron-sulfur cluster assembly 2 homolog, mitochondrial (protein), ISCA2, Homo sapiens
Function / homology
Function and homology information


mitochondrial [4Fe-4S] assembly complex / : / Mitochondrial iron-sulfur cluster biogenesis / Maturation of TCA enzymes and regulation of TCA cycle / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / mitochondrial matrix / iron ion binding / mitochondrion / identical protein binding
Similarity search - Function
FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / FeS cluster insertion protein / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis
Similarity search - Domain/homology
Iron-sulfur cluster assembly 2 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Stefano Da Vela (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 #3572
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.063
Search similar-shape structures of this assembly by Omokage search (details)
Model #3573
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.136
Search similar-shape structures of this assembly by Omokage search (details)
Model #3574
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.216
Search similar-shape structures of this assembly by Omokage search (details)
Model #3575
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.049
Search similar-shape structures of this assembly by Omokage search (details)
Model #3576
Type: dummy / Radius of dummy atoms: 1.90 A
Comment: Monsa model (together with the complex, see entry SASDGF2)
Chi-square value: 0.961
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Human mitochondrial iron-sulfur cluster assembly ISCA2 protein
BufferName: 50 mM phosphate, 150 mM NaCl, 5 mM DTT / pH: 7
Entity #1802Name: ISCA2 / Type: protein
Description: Iron-sulfur cluster assembly 2 homolog, mitochondrial
Formula weight: 12.041 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q86U28
Sequence:
EAGEGQIRLT DSCVQRLLEI TEGSEFLRLQ VEGGGCSGFQ YKFSLDTVIN PDDRVFEQGG ARVVVDSDSL AFVKGAQVDF SQELIRSSFQ VLNNPQAQQG CSCGSSFSIK L

-
Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 6M
Scan
Title: Human mitochondrial iron-sulfur cluster assembly ISCA2 protein
Measurement date: Sep 16, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 0.995 sec. / Number of frames: 2400 / Unit: 1/nm /
MinMax
Q0.1034 7.3052
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1378 /
MinMax
Q0.133847 3.93923
P(R) point1 1378
R0 6.65
Result
Type of curve: sec /
ExperimentalPorod
MW18.7 kDa19 kDa
Volume-31 nm3

P(R)GuinierGuinier error
Forward scattering, I089.45 89 0.3
Radius of gyration, Rg2.07 nm2.03 nm0.049

MinMax
D-6.65
Guinier point12 195

+
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