[English] 日本語
Yorodumi
- SASDGV9: Nucleolar RNA helicase 2 (DDX21) fragment 186-783 (Nucleolar RNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGV9
SampleNucleolar RNA helicase 2 (DDX21) fragment 186-783
  • Nucleolar RNA helicase 2 fragment 186-783 (protein), DDx21 fragment 186-7, Homo sapiens
Function / homology
Function and homology information


RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase III / snoRNA binding / response to exogenous dsRNA ...RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase III / snoRNA binding / response to exogenous dsRNA / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / B-WICH complex positively regulates rRNA expression / rRNA processing / osteoblast differentiation / double-stranded RNA binding / chromosome / defense response to virus / transcription by RNA polymerase II / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / rRNA binding / RNA helicase / chromatin remodeling / innate immune response / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
GUCT / GUCT (NUC152) domain / : / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...GUCT / GUCT (NUC152) domain / : / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nucleolar RNA helicase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Maria Josefina Marcaida (École polytechnique fédérale de Lausanne (EPFL), Switzerland)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2552
Type: dummy / Software: (r9988) / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.227 / P-value: 0.023503

-
Sample

SampleName: Nucleolar RNA helicase 2 (DDX21) fragment 186-783 / Specimen concentration: 10 mg/ml
BufferName: 20 mM HEPES, 500 mM NaCl, 10 % Glycerol, 2 mM TCEP / pH: 7.5
Entity #1346Name: DDx21 fragment 186-7 / Type: protein / Description: Nucleolar RNA helicase 2 fragment 186-783 / Formula weight: 68.754 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q9NR30
Sequence: MGSSHHHHHH SQDPENLYFQ GAFSNFPISE ETIKLLKGRG VTFLFPIQAK TFHHVYSGKD LIAQARTGTG KTFSFAIPLI EKLHGELQDR KRGRAPQVLV LAPTRELANQ VSKDFSDITK KLSVACFYGG TPYGGQFERM RNGIDILVGT PGRIKDHIQN GKLDLTKLKH ...Sequence:
MGSSHHHHHH SQDPENLYFQ GAFSNFPISE ETIKLLKGRG VTFLFPIQAK TFHHVYSGKD LIAQARTGTG KTFSFAIPLI EKLHGELQDR KRGRAPQVLV LAPTRELANQ VSKDFSDITK KLSVACFYGG TPYGGQFERM RNGIDILVGT PGRIKDHIQN GKLDLTKLKH VVLDEVDQML DMGFADQVEE ILSVAYKKDS EDNPQTLLFS ATCPHWVFNV AKKYMKSTYE QVDLIGKKTQ KTAITVEHLA IKCHWTQRAA VIGDVIRVYS GHQGRTIIFC ETKKEAQELS QNSAIKQDAQ SLHGDIPQKQ REITLKGFRN GSFGVLVATN VAARGLDIPE VDLVIQSSPP KDVESYIHRS GRTGRAGRTG VCICFYQHKE EYQLVQVEQK AGIKFKRIGV PSATEIIKAS SKDAIRLLDS VPPTAISHFK QSAEKLIEEK GAVEALAAAL AHISGATSVD QRSLINSNVG FVTMILQCSI EMPNISYAWK ELKEQLGEEI DSKVKGMVFL KGKLGVCFDV PTASVTEIQE KWHDSRRWQL SVATEQPELE GPREGYGGFR GQREGSRGFR GQRDGNRRFR GQREGSRGPR GQRSGGGNKS NRSQNKGQKR SFSKAFGQ

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.867 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Nucleolar RNA helicase 2 (DDX21) fragment 186-783 / Measurement date: Mar 4, 2018 / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 3000 / Unit: 1/A /
MinMax
Q0.0075 0.3787
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 792 /
MinMax
Q0.00748023 0.378722
P(R) point1 792
R0 176
Result
Type of curve: sec /
ExperimentalPorod
MW156 kDa185 kDa
Volume-297 nm3

P(R)GuinierGuinier error
Forward scattering, I079.32 78.81 0.086
Radius of gyration, Rg4.88 nm4.76 nm0.02

MinMax
D-17.6
Guinier point1 43

+
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