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- PDB-1t2s: Structural basis for 3' end recognition of nucleic acids by the D... -

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Basic information

Entry
Database: PDB / ID: 1t2s
TitleStructural basis for 3' end recognition of nucleic acids by the Drosophila Argonaute 2 PAZ domain
Components
  • 5'-D(*CP*TP*CP*AP*C)-3'
  • Argonaute 2
Keywordsnucleic acid binding protein/dna / nucleic acid binding protein / dna / nucleic acid binding protein-dna COMPLEX
Function / homology
Function and homology information


syncytial nuclear migration / RNAi-mediated antiviral immunity against RNA virus / Post-transcriptional silencing by small RNAs / cellularization / siRNA-mediated heterochromatin formation / pole cell formation / MicroRNA (miRNA) biogenesis / segment polarity determination / RNAi-mediated antiviral immune response / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism ...syncytial nuclear migration / RNAi-mediated antiviral immunity against RNA virus / Post-transcriptional silencing by small RNAs / cellularization / siRNA-mediated heterochromatin formation / pole cell formation / MicroRNA (miRNA) biogenesis / segment polarity determination / RNAi-mediated antiviral immune response / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Small interfering RNA (siRNA) biogenesis / Transcriptional regulation by small RNAs / neuronal ribonucleoprotein granule / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / piRNA-mediated gene silencing by mRNA destabilization / dosage compensation by hyperactivation of X chromosome / piRNA processing / siRNA-mediated pericentric heterochromatin formation / miRNA-mediated post-transcriptional gene silencing / RISC-loading complex / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / siRNA binding / RISC complex / miRNA binding / negative regulation of viral genome replication / RNA endonuclease activity / cellular response to virus / cytoplasmic ribonucleoprotein granule / defense response to virus / single-stranded RNA binding / metal ion binding / nucleus / cytoplasm / cytosol
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 profile. / Piwi domain / 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
DNA / Protein argonaute-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsLingel, A. / Simon, B. / Izaurralde, E. / Sattler, M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain.
Authors: Lingel, A. / Simon, B. / Izaurralde, E. / Sattler, M.
#1: Journal: 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
DepositionApr 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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
Remark 999SEQUENCE RESIDUES 1-4 IN THE CONSTRUCT USED FOR THE STRUCTURE DETERMINATION ARE FROM THE EXPRESSION VECTOR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*CP*TP*CP*AP*C)-3'
A: Argonaute 2


Theoretical massNumber of molelcules
Total (without water)15,3692
Polymers15,3692
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 / 150LOWEST ENERGIES
RepresentativeModel #1lowest energies

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Components

#1: DNA chain 5'-D(*CP*TP*CP*AP*C)-3'


Mass: 1439.988 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Argonaute 2 / CG7439 PROTEIN


Mass: 13928.974 Da / Num. of mol.: 1 / Fragment: paz domain, residues 605-723
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PETM60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VUQ5

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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 AND EDITED FILTERED NOESY EXPERIMENTS

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Sample preparation

DetailsContents: 0.2-1 MM 15N OR 15N,13C-LABELED PROTEIN, 0.1-2.5 MM UNLABELED DNA, 50 MM SODIUM PHOSPHATE BUFFER, 0.2 MM DTT
Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 295 K

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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 DRXBrukerDRX9003

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Processing

NMR software
NameDeveloperClassification
ARIA1.2, CNS1.1NILGES, BRUNGER ET AL.refinement
NMRViewstructure solution
ARIA/CNSstructure solution
RefinementMethod: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: THE EXPERIMENTALLY DETERMINED DISTANCE RESTRAINTS WERE APPLIED IN A MIXED TORSION AND CARTESIA DYNAMICS SIMULATED ANNEALING PROTOCOL. THE FINAL STRUCTURE ENSEMBLE WAS REFINED IN A SHELL OF WATER MOLECULES.
NMR representativeSelection criteria: lowest energies
NMR ensembleConformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 150 / Conformers submitted total number: 10

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