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- PDB-1r4k: Solution Structure of the Drosophila Argonaute 1 PAZ Domain -

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Basic information

Entry
Database: PDB / ID: 1r4k
TitleSolution Structure of the Drosophila Argonaute 1 PAZ Domain
ComponentsArgonaute 1
KeywordsRNA BINDING PROTEIN / beta barrel
Function / homology
Function and homology information


regulation of olfactory learning / Post-transcriptional silencing by small RNAs / female germ-line stem cell population maintenance / germarium-derived female germ-line cyst formation / germarium-derived oocyte fate determination / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / Transcriptional regulation by small RNAs / RNA endonuclease activity, producing 5'-phosphomonoesters / endoribonuclease activity, cleaving miRNA-paired mRNA ...regulation of olfactory learning / Post-transcriptional silencing by small RNAs / female germ-line stem cell population maintenance / germarium-derived female germ-line cyst formation / germarium-derived oocyte fate determination / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / Transcriptional regulation by small RNAs / RNA endonuclease activity, producing 5'-phosphomonoesters / endoribonuclease activity, cleaving miRNA-paired mRNA / segment polarity determination / miRNA-mediated gene silencing by mRNA destabilization / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / habituation / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / RISC complex / miRNA binding / mRNA catabolic process / RNA endonuclease activity / P-body / heterochromatin formation / cytoplasmic ribonucleoprotein granule / nucleic acid binding / negative regulation of translation / single-stranded RNA binding / ribonucleoprotein complex / perinuclear region of cytoplasm / enzyme binding / nucleus / 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 / PAZ domain / PAZ domain profile. / PAZ domain / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
Argonaute-1, isoform A / :
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR
AuthorsYan, K.S. / Yan, S. / Farooq, A. / Han, A. / Zeng, L. / Zhou, M.-M.
CitationJournal: Nature / Year: 2003
Title: Structure and conserved RNA binding of the PAZ domain
Authors: Yan, K.S. / Yan, S. / Farooq, A. / Han, A. / Zeng, L. / Zhou, M.-M.
History
DepositionOct 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Argonaute 1


Theoretical massNumber of molelcules
Total (without water)19,7991
Polymers19,7991
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)1 / -
RepresentativeModel #1lowest energy structure

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Components

#1: Protein Argonaute 1


Mass: 19799.145 Da / Num. of mol.: 1 / Fragment: PAZ Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ago1 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9V6V6, UniProt: Q32KD4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 0.5mM Ago1 PAZ Domain, 100mM sodium phosphate, 150mM NaCl, 5mM DTT-d10
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM sodium phosphate, 150mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe3.1Delaglioprocessing
NMRView5Johnsondata analysis
X-PLOR3.1Brungerstructure solution
ARIA1.2Nilgesstructure solution
ARIA1.2Nilgesrefinement
NMR representativeSelection criteria: lowest energy structure
NMR ensembleConformers submitted total number: 1

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