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- PDB-1vyn: STRUCTURE AND NUCLEIC ACID BINDING OF THE DROSOPHILA ARGONAUTE2 P... -

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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 / RNAi-mediated antiviral immunity against RNA virus / Post-transcriptional silencing by small RNAs / cellularization / MicroRNA (miRNA) biogenesis / pole cell formation / RNAi-mediated antiviral immune response / Small interfering RNA (siRNA) biogenesis / RNA endonuclease activity, producing 5'-phosphomonoesters / Transcriptional regulation by small RNAs ...syncytial nuclear migration / RNAi-mediated antiviral immunity against RNA virus / Post-transcriptional silencing by small RNAs / cellularization / MicroRNA (miRNA) biogenesis / pole cell formation / RNAi-mediated antiviral immune response / Small interfering RNA (siRNA) biogenesis / RNA endonuclease activity, producing 5'-phosphomonoesters / Transcriptional regulation by small RNAs / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / segment polarity determination / neuronal ribonucleoprotein granule / dsRNA transport / dosage compensation by hyperactivation of X chromosome / siRNA-mediated pericentric heterochromatin formation / 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 / cytoplasmic ribonucleoprotein granule / defense response to virus / single-stranded RNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
paz domain / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 ...paz domain / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / 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 profile. / PAZ domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGONAUTE2


Theoretical massNumber of molelcules
Total (without water)16,0661
Polymers16,0661
Non-polymers00
Water00
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

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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.

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Experimental details

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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.

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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

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NMR measurement

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

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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

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