[English] 日本語
Yorodumi
- PDB-1vyn: STRUCTURE AND NUCLEIC ACID BINDING OF THE DROSOPHILA ARGONAUTE2 P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vyn
TitleSTRUCTURE AND NUCLEIC ACID BINDING OF THE DROSOPHILA ARGONAUTE2 PAZ DOMAIN
ComponentsARGONAUTE2
KeywordsNUCLEIC ACID BINDING / RNA INTERFERENCE
Function / homology
Function and homology information


syncytial nuclear migration / Post-transcriptional silencing by small RNAs / cellularization / siRNA-mediated retrotransposon silencing by heterochromatin formation / RNAi-mediated antiviral immune response / MicroRNA (miRNA) biogenesis / RNA endonuclease activity, producing 5'-phosphomonoesters / pole cell formation / Small interfering RNA (siRNA) biogenesis / endoribonuclease activity, cleaving siRNA-paired mRNA ...syncytial nuclear migration / Post-transcriptional silencing by small RNAs / cellularization / siRNA-mediated retrotransposon silencing by heterochromatin formation / RNAi-mediated antiviral immune response / MicroRNA (miRNA) biogenesis / RNA endonuclease activity, producing 5'-phosphomonoesters / pole cell formation / Small interfering RNA (siRNA) biogenesis / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / segment polarity determination / neuronal ribonucleoprotein granule / messenger ribonucleoprotein complex / dsRNA transport / dosage compensation by hyperactivation of X chromosome / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / siRNA binding / RISC complex / negative regulation of viral genome replication / RNA endonuclease activity / cellular response to virus / defense response to virus / single-stranded RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 ...paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain / PAZ domain / PAZ domain profile. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsLingel, A. / Simon, B. / Izaurralde, E. / Sattler, M.
CitationJournal: Nature / Year: 2003
Title: Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain.
Authors: Lingel, A. / Simon, B. / Izaurralde, E. / Sattler, M.
History
DepositionMay 3, 2004Deposition site: PDBE / Processing site: PDBE
SupersessionMay 11, 2004ID: 1UPO
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ARGONAUTE2


Theoretical massNumber of molelcules
Total (without water)16,0661
Polymers16,0661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LOWEST ENERGIES
RepresentativeModel #8

-
Components

#1: Protein ARGONAUTE2


Mass: 16066.420 Da / Num. of mol.: 1 / Fragment: PAZ DOMAIN, RESIDUES 605-743
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VUQ5
Sequence detailsRESIDUES 1-4 IN THE CONSTRUCT USED FOR THE STRUCTURE DETERMINATION ARE FROM THE EXPRESSION VECTOR.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
121NOESY
NMR detailsText: STRUCTURAL RESTRAINTS WERE DERIVED FROM 13C AND 15N-EDITED NOESY EXPERIMENTS, J-COUPLINGS, AND H-N RESIDUAL DIPOLAR COUPLINGS.

-
Sample preparation

DetailsContents: 1.0-1.5 MM 15N OR 15N,13C-LABELED PROTEIN, 50 MM NA.PHOSPHATE BUFFER, 150 MM NACL, 0.2 MM DTT
Sample conditionsIonic strength: 150 mM NaCl mM / pH: 6.8 / Pressure: 1 atm / Temperature: 295 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7003
Bruker DRXBrukerDRX9004

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2, CNS1.1 CNS1.1CNS1.1NILGES, BRUNGER ET AL.refinement
NMRViewstructure solution
ARIA/CNSstructure solution
RefinementMethod: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: THE NMR ENSEMBLE HAS BEEN REFINED IN A SHELL OF WATER MOLECULES.REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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