[English] 日本語
Yorodumi
- SASDAB2: Cytochrome c from equine heart (Cytochrome c, CytoC + Heme C) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDAB2
SampleCytochrome c from equine heart
  • Cytochrome c (protein), CytoC, Equus caballus
  • Heme C (other), Heme C
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / apoptotic process / lipid binding / heme binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Biological speciesEquus caballus (horse)
Contact author
  • Cy M Jeffries (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 #15
Type: atomic / Software: (2.8.3) / Radius of dummy atoms: 1.90 A / Comment: 1AKK / Chi-square value: 1.068
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Cytochrome c from equine heart / Purity method: gel filtration / Sample MW: 35.3 kDa / Specimen concentration: 10 mg/ml / Concentration method: nanodrop / Entity id: 1445 / 1446
BufferName: 25 mM HEPES, 100 mM NaCl, 3% v/v glycerol / pH: 7.5
Entity #1445Name: CytoC / Type: protein / Description: Cytochrome c / Formula weight: 11.701 / Num. of mol.: 1 / Source: Equus caballus / References: UniProt: P00004
Sequence:
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGFTYTD ANKNKGITWK EETLMEYLEN PKKYIPGTKM IFAGIKKKTE REDLIAYLKK ATNE
Entity #1446Name: Heme C / Type: other / Description: Heme C / Formula weight: 0.618 / Num. of mol.: 1
Sequence:
C34H34FeN4 O4

-
Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 6M
Scan
Title: Cytochrome c from equine heart / Measurement date: Apr 8, 2018 / Storage temperature: 20 °C / Cell temperature: 10 °C / Exposure time: 0.5 sec. / Number of frames: 58 / Unit: 1/nm /
MinMax
Q0.1512 6.921
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 2185 /
MinMax
Q0.151155 6.17122
P(R) point1 2185
R0 3.66
Result
Type of curve: sec /
ExperimentalPorod
MW10 kDa8.5 kDa
Volume-11.5 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I01211 1.44 1206.41 1.63
Radius of gyration, Rg1.3 nm0.002 1.3 nm0.02

MinMax
D-3.66
Guinier point7 301

+
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