[English] 日本語
Yorodumi
- SASDFH5: DPCD His-RuvBl1/RuvBl2 hexamer complex (Protein DPCD + RuvB-like ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFH5
SampleDPCD His-RuvBl1/RuvBl2 hexamer complex
  • Protein DPCD (protein), Homo sapiens
  • RuvB-like 1 (protein), Homo sapiens
  • RuvB-like 2 (protein), Homo sapiens
Function / homology
Function and homology information


third ventricle development / left/right pattern formation / promoter-enhancer loop anchoring activity / epithelial cilium movement involved in extracellular fluid movement / lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / flagellated sperm motility / R2TP complex ...third ventricle development / left/right pattern formation / promoter-enhancer loop anchoring activity / epithelial cilium movement involved in extracellular fluid movement / lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / flagellated sperm motility / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / protein folding chaperone complex / determination of left/right symmetry / box C/D snoRNP assembly / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / DNA helicase activity / positive regulation of DNA repair / TBP-class protein binding / telomere maintenance / cellular response to estradiol stimulus / establishment of localization in cell / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / ADP binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / DNA helicase / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / cadherin binding / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein DPCD / DPCD protein family / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein DPCD / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Raphael Dos Santos Morais (University of Lorraine)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2935
Type: dummy / Radius of dummy atoms: 2.90 A / Chi-square value: 1.507 / P-value: 0.347397

-
Sample

SampleName: DPCD His-RuvBl1/RuvBl2 hexamer complex / Specimen concentration: 4 mg/ml / Entity id: 1607 / 1611 / 1612
BufferName: HEPES 20 mM, NaCl 150 mM, Glycerol 1%, TCEP 5 mM / pH: 7.5
Entity #1607Type: protein / Description: Protein DPCD / Formula weight: 23.505 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q9BVM2
Sequence: GPHMAVTGWL ESLRTAQKTA LLQDGRRKVH YLFPDGKEMA EEYDEKTSEL LVRKWRVKSA LGAMGQWQLE VGDPAPLGAG NLGPELIKES NANPIFMRKD TKMSFQWRIR NLPYPKDVYS VSVDQKERCI IVRTTNKKYY KKFSIPDLDR HQLPLDDASL SFAHANCTLI ...Sequence:
GPHMAVTGWL ESLRTAQKTA LLQDGRRKVH YLFPDGKEMA EEYDEKTSEL LVRKWRVKSA LGAMGQWQLE VGDPAPLGAG NLGPELIKES NANPIFMRKD TKMSFQWRIR NLPYPKDVYS VSVDQKERCI IVRTTNKKYY KKFSIPDLDR HQLPLDDASL SFAHANCTLI ISYQKPKEVV VAESELQKEL KKVKTAHSND GDCKTQ
Entity #1611Type: protein / Description: RuvB-like 1 / Formula weight: 51.759 / Num. of mol.: 3 / Source: Homo sapiens / References: UniProt: Q9Y265
Sequence: MVHHHHHHLV PRGSKIEEVK STTKTQRIAS HSHVKGLGLD ESGLAKQAAS GLVGQENARE ACGVIVELIK SKKMAGRAVL LAGPPGTGKT ALALAIAQEL GSKVPFCPMV GSEVYSTEIK KTEVLMENFR RAIGLRIKET KEVYEGEVTE LTPCETENPM GGYGKTISHV ...Sequence:
MVHHHHHHLV PRGSKIEEVK STTKTQRIAS HSHVKGLGLD ESGLAKQAAS GLVGQENARE ACGVIVELIK SKKMAGRAVL LAGPPGTGKT ALALAIAQEL GSKVPFCPMV GSEVYSTEIK KTEVLMENFR RAIGLRIKET KEVYEGEVTE LTPCETENPM GGYGKTISHV IIGLKTAKGT KQLKLDPSIF ESLQKERVEA GDVIYIEANS GAVKRQGRCD TYATEFDLEA EEYVPLPKGD VHKKKEIIQD VTLHDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALESSIAPIV IFASNRGNCV IRGTEDITSP HGIPLDLLDR VMIIRTMLYT PQEMKQIIKI RAQTEGINIS EEALNHLGEI GTKTTLRYSV QLLTPANLLA KINGKDSIEK EHVEEISELF YDAKSSAKIL ADQQDKYMK
Entity #1612Type: protein / Description: RuvB-like 2 / Formula weight: 51.886 / Num. of mol.: 3 / Source: Homo sapiens / References: UniProt: Q9Y230
Sequence: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMGM AQALGPDTPF TAIAGSEIFS LEMSKTEALT QAFRRSIGVR IKEETEIIEG EVVEIQIDRP ATGTGSKVGK LTLKTTEMET ...Sequence:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMGM AQALGPDTPF TAIAGSEIFS LEMSKTEALT QAFRRSIGVR IKEETEIIEG EVVEIQIDRP ATGTGSKVGK LTLKTTEMET IYDLGTKMIE SLTKDKVQAG DVITIDKATG KISKLGRSFT RARDYDAMGS QTKFVQCPDG ELQKRKEVVH TVSLHEIDVI NSRTQGFLAL FSGDTGEIKS EVREQINAKV AEWREEGKAE IIPGVLFIDE VHMLDIESFS FLNRALESDM APVLIMATNR GITRIRGTSY QSPHGIPIDL LDRLLIVSTT PYSEKDTKQI LRIRCEEEDV EMSEDAYTVL TRIGLETSLR YAIQLITAAS LVCRKRKGTE VQVDDIKRVY SLFLDESRST QYMKEYQDAF LFNELKGETM DTSLEVLFQ

-
Experimental information

BeamInstrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 2 mm
DetectorName: Eiger 4M / Pixsize x: 75 mm
Scan
Title: DPCD His-RuvBl1/RuvBl2 hexamer complex / Measurement date: Mar 21, 2019 / Cell temperature: 15 °C / Exposure time: 1 sec. / Number of frames: 41 / Unit: 1/A /
MinMax
Q0.0041 0.5782
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 442 /
MinMax
Q0.00775358 0.208798
P(R) point1 442
R0 159
Result
Type of curve: sec
Comments: The experimental molecular weight was determined from SEC-RALS/LALS experiment (370 kDa).
ExperimentalPorod
MW370 kDa-
Volume-856 nm3

P(R)GuinierGuinier error
Forward scattering, I00.09084 0.09066 5.0E-5
Radius of gyration, Rg5.33 nm5.39 nm0.04

MinMax
D-15.9
Guinier point5 44

+
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://pdbjlvh1.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