[English] 日本語
Yorodumi
- SASDGD2: Putative mitochondrial transferase CAF17: human IBA57 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGD2
SamplePutative mitochondrial transferase CAF17: human IBA57
  • Putative transferase CAF17, mitochondrial (protein), IBA57, Homo sapiens
Function / homology
Function and homology information


heme biosynthetic process / iron-sulfur cluster assembly / transferase activity / mitochondrial matrix / mitochondrion / RNA binding
Similarity search - Function
CAF17, C-terminal beta-barrel domain / YgfZ/GcvT conserved site / YgfZ/GcvT / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
Similarity search - Domain/homology
Iron-sulfur cluster assembly factor IBA57, 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 #3571
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.075
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Putative mitochondrial transferase CAF17: human IBA57 / Specimen concentration: 5 mg/ml
BufferName: 50 mM phosphate, 150 mM NaCl, 5 mM DTT / pH: 7
Entity #1801Name: IBA57 / Type: protein / Description: Putative transferase CAF17, mitochondrial / Formula weight: 33.242 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q5T440
Sequence: AGAAWACFRL DGRTLLRVRG PDAAPFLLGL LTNELPLPSP AAAGAPPAAR AGYAHFLNVQ GRTLYDVILY GLQEHSEVSG FLLECDSSVQ GALQKHLALY RIRRKVTVEP HPELRVWAVL PSSPEACGAA SLQERAGAAA ILIRDPRTAR MGWRLLTQDE GPALVPGGRL ...Sequence:
AGAAWACFRL DGRTLLRVRG PDAAPFLLGL LTNELPLPSP AAAGAPPAAR AGYAHFLNVQ GRTLYDVILY GLQEHSEVSG FLLECDSSVQ GALQKHLALY RIRRKVTVEP HPELRVWAVL PSSPEACGAA SLQERAGAAA ILIRDPRTAR MGWRLLTQDE GPALVPGGRL GDLWDYHQHR YLQGVPEGVR DLPPGVALPL ESNLAFMNGV SFTKGCYIGQ ELTARTHHMG VIRKRLFPVR FLDPLPTSGI TPGATVLTAS GQTVGKFRAG QGNVGLALLW SEKIKGPLHI RASEGAQVAL AASVPDWWP

-
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: Putative mitochondrial transferase CAF17: human IBA57
Measurement date: Jul 10, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 0.995 sec. / Number of frames: 3000 / Unit: 1/nm /
MinMax
Q0.1226 3.6959
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1296 /
MinMax
Q0.122607 3.69587
P(R) point1 1296
R0 7.14
Result
Type of curve: sec /
ExperimentalPorod
MW25.6 kDa31 kDa
Volume-50 nm3

P(R)GuinierGuinier error
Forward scattering, I0177.3 177 0.39
Radius of gyration, Rg2.172 nm2.16 nm0.015

MinMax
D-7.14
Guinier point3 174

+
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