[English] 日本語
Yorodumi
- SASDFL7: Complex with 1H histone chaperone Asf1, histones H3 and H4, 2H ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFL7
SampleComplex with 1H histone chaperone Asf1, histones H3 and H4, 2H acetyltransferase Rtt109 and histone chaperone Vps75 (1-225aa) in 42% v/v D2O
  • Vacuolar protein sorting-associated protein 75 (1-225 aa)Vacuole (protein), Vps75 1-225, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
  • Histone acetyltransferase RTT109 (protein), Rtt109, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
  • Histone chaperone ASF1 (protein), Asf1
  • Histone H4 (protein), H4, Xenopus laevis
  • Histone H3 full-length (protein), H3 FL, Xenopus laevis
Function / homology
Function and homology information


: / : / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex ...: / : / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex / : / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / acetyltransferase activator activity / peptidyl-lysine acetylation / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity / retrotransposon silencing / DNA replication-dependent chromatin assembly / nucleosome disassembly / histone H3K27 acetyltransferase activity / : / silent mating-type cassette heterochromatin formation / peptide-lysine-N-acetyltransferase activity / protein acetylation / subtelomeric heterochromatin formation / negative regulation of DNA damage checkpoint / regulation of DNA repair / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / protein transport / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / protein heterodimerization activity / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP ...Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone chaperone ASF1 / Vacuolar protein sorting-associated protein 75 / Histone H4 / Histone acetyltransferase RTT109 / Histone H3.3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Xenopus laevis (African clawed frog)
Contact author
  • Nataliya Danilenko (Leibniz University of Hannover, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3176
Type: atomic / Chi-square value: 0.941 / P-value: 0.000001
Search similar-shape structures of this assembly by Omokage search (details)
Model #3177
Type: atomic / Chi-square value: 2.848 / P-value: 0.000001
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Complex with 1H histone chaperone Asf1, histones H3 and H4, 2H acetyltransferase Rtt109 and histone chaperone Vps75 (1-225aa) in 42% v/v D2O
Specimen concentration: 4 mg/ml / Entity id: 1488 / 1489 / 1490 / 1492 / 1728
BufferName: 50 mM citrate, 150 mM NaCl, 5 mM BME, 42% D2O / pH: 6.5
Entity #1488Name: Vps75 1-225 / Type: protein
Description: Vacuolar protein sorting-associated protein 75 (1-225 aa)Vacuole
Formula weight: 26.554 / Num. of mol.: 2
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P53853
Sequence: MMSDQENENE HAKAFLGLAK CEEEVDAIER EVELYRLNKM KPVYEKRDAY IDEIAEFWKI VLSQHVSFAN YIRASDFKYI DTIDKIKVEW LALESEMYDT RDFSITFHFH GIEGDFKEQQ VTKVFQIKKG KDDQEDGILT SEPVPIEWPQ SYDSINPDLI KDKRSPEGKK ...Sequence:
MMSDQENENE HAKAFLGLAK CEEEVDAIER EVELYRLNKM KPVYEKRDAY IDEIAEFWKI VLSQHVSFAN YIRASDFKYI DTIDKIKVEW LALESEMYDT RDFSITFHFH GIEGDFKEQQ VTKVFQIKKG KDDQEDGILT SEPVPIEWPQ SYDSINPDLI KDKRSPEGKK KYRQGMKTIF GWFRWTGLKP GKEFPHGDSL ASLFSEEIYP FCVKYYAEAQ RDLED
Entity #1489Name: Rtt109 / Type: protein / Description: Histone acetyltransferase RTT109 / Formula weight: 50.095 / Num. of mol.: 1
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q07794
Sequence: MSLNDFLSSV LPVSEQFEYL SLQSIPLETH AVVTPNKDDK RVPKSTIKTQ HFFSLFHQGK VFFSLEVYVY VTLWDEADAE RLIFVSKADT NGYCNTRVSV RDITKIILEF ILSIDPNYYL QKVKPAIRSY KKISPELISA ASTPARTLRI LARRLKQSGS TVLKEIESPR ...Sequence:
MSLNDFLSSV LPVSEQFEYL SLQSIPLETH AVVTPNKDDK RVPKSTIKTQ HFFSLFHQGK VFFSLEVYVY VTLWDEADAE RLIFVSKADT NGYCNTRVSV RDITKIILEF ILSIDPNYYL QKVKPAIRSY KKISPELISA ASTPARTLRI LARRLKQSGS TVLKEIESPR FQQDLYLSFT CPREILTKIC LFTRPASQYL FPDSSKNSKK HILNGEELMK WWGFILDRLL IECFQNDTQA KLRIPGEDPA RVRSYLRGMK YPLWQVGDIF TSKENSLAVY NIPLFPDDPK ARFIHQLAEE DRLLKVSLSS FWIELQERQE FKLSVTSSVM GISGYSLATP SLFPSSADVI VPKSRKQFRA IKKYITGEEY DTEEGAIEAF TNIRDFLLLR MATNLQSLTG KREHRERNQP VPASNINTLA ITMLKPRKKA KALPKT
Entity #1490Name: Asf1 / Type: protein / Description: Histone chaperone ASF1 / Formula weight: 19.125 / Num. of mol.: 1 / References: UniProt: P32447
Sequence:
MSIVSLLGIK VLNNPAKFTD PYEFEITFEC LESLKHDLEW KLTYVGSSRS LDHDQELDSI LVGPVPVGVN KFVFSADPPS AELIPASELV SVTVILLSCS YDGREFVRVG YYVNNEYDEE ELRENPPAKV QVDHIVRNIL AEKPRVTRFN IVWDNENEGD LYPPEQPGV
Entity #1492Name: H4 / Type: protein / Description: Histone H4 / Formula weight: 11.367 / Num. of mol.: 1 / Source: Xenopus laevis / References: UniProt: P62799
Sequence:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG
Entity #1728Name: H3 FL / Type: protein / Description: Histone H3 full-length / Formula weight: 15.328 / Num. of mol.: 1 / Source: Xenopus laevis / References: UniProt: Q6PI79
Sequence:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

-
Experimental information

BeamInstrument name: ILL D22 / City: Grenoble / 国: France / Type of source: neutron source / Wavelength: 0.6 Å / Dist. spec. to detc.: 4 mm
DetectorName: 128 linear sensitive Reuter-Stokes detector / Type: 3He multidetector / Pixsize x: 0.8 mm
Scan
Title: Complex with 1H histone chaperone Asf1, histones H3 and H4, 2H acetyltransferase Rtt109 and histone chaperone Vps75 (1-225aa) in 42% v/v D2O
Measurement date: Nov 14, 2016 / Cell temperature: 25.2 °C / Exposure time: 3600 sec. / Number of frames: 1 / Unit: 1/A /
MinMax
Q0.0144 0.2424
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 90 /
MinMax
Q0.01438 0.2009
P(R) point1 90
R0 105
Result
Experimental MW: 149 kDa / Type of curve: single_conc
P(R)GuinierGuinier error
Forward scattering, I00.5464 0.55 0.0012
Radius of gyration, Rg3.32 nm3.365 nm0.028

MinMax
D-10.5
Guinier point1 12

+
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