[English] 日本語
Yorodumi
- SASDFX3: Semi-synthetic nucleosome core particle (NCP) (Histone H3, H3 + H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFX3
SampleSemi-synthetic nucleosome core particle (NCP)
  • Histone H3 (protein), H3, Xenopus laevis
  • Histone H4 (protein), H4, Xenopus laevis
  • Histone H2a (protein), H2a, Xenopus laevis
  • Histone H2b (protein), H2b, Xenopus laevis
  • 147bp 601 Widom sequence (DNA), 601-147bp, synthetic construct
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Semi-synthetic nucleosome core particle (NCP) / Specimen concentration: 1.8 mg/ml / Entity id: 1520 / 1521 / 1522 / 1523 / 1524
BufferName: 15 mM HEPES, 200 mM NaCl / pH: 7.3
Entity #1520Name: H3 / Type: protein / Description: Histone H3 / Formula weight: 15.271 / Num. of mol.: 2 / Source: Xenopus laevis
Sequence:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA
Entity #1521Name: H4 / Type: protein / Description: Histone H4 / Formula weight: 11.236 / Num. of mol.: 2 / Source: Xenopus laevis
Sequence:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG
Entity #1522Name: H2a / Type: protein / Description: Histone H2a / Formula weight: 13.95 / Num. of mol.: 2 / Source: Xenopus laevis
Sequence:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK
Entity #1523Name: H2b / Type: protein / Description: Histone H2b / Formula weight: 13.494 / Num. of mol.: 2 / Source: Xenopus laevis
Sequence:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK
Entity #1524Name: 601-147bp / Type: DNA / Description: 147bp 601 Widom sequence / Formula weight: 45.202 / Num. of mol.: 1 / Source: synthetic construct
Sequence:
ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCCGAT

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 2.87 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
ScanTitle: Semi-synthetic nucleosome core particle (NCP) / Measurement date: Dec 11, 2017 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 243 / Unit: 1/nm /
MinMax
Q0.0714 2.8524
ResultType of curve: sec /
ExperimentalPorod
MW200 kDa-
Volume-353 nm3

P(R)GuinierGuinier error
Forward scattering, I090.55 91.26 0.1
Radius of gyration, Rg4.268 nm4.35 nm0.01

MinMax
D-12.8
Guinier point15 56

+
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://pdbjlc1.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