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- PDB-2xfm: Complex structure of the MIWI Paz domain bound to methylated sing... -

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Basic information

Entry
Database: PDB / ID: 2xfm
TitleComplex structure of the MIWI Paz domain bound to methylated single stranded RNA
Components
  • 5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3'
  • PIWI-LIKE PROTEIN 1
KeywordsRNA/PROTEIN / RNA-PROTEIN COMPLEX / DIFFERENTIATION / RNA INTERFERENCE
Function / homology
Function and homology information


primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / spermatid development / RNA endonuclease activity / meiotic cell cycle / regulation of translation / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GAGE / GAGE protein / GAGE / paz domain / paz domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain ...GAGE / GAGE protein / GAGE / paz domain / paz domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / Piwi-like protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / ARIA
AuthorsSimon, B. / Kirkpatrick, J.P. / Eckhardt, S. / Sehr, P. / Andrade-Navarro, M.A. / Pillai, R.S. / Carlomagno, T.
CitationJournal: Structure / Year: 2011
Title: Recognition of 2'-O-Methylated 3'-End of Pirna by the Paz Domain of a Piwi Protein.
Authors: Simon, B. / Kirkpatrick, J.P. / Eckhardt, S. / Reuter, M. / Rocha, E.A. / Andrade-Navarro, M.A. / Sehr, P. / Pillai, R.S. / Carlomagno, T.
History
DepositionMay 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Derived calculations / Version format compliance
Revision 2.0May 15, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PIWI-LIKE PROTEIN 1
B: 5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3'


Theoretical massNumber of molelcules
Total (without water)20,1422
Polymers20,1422
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LOWEST ENERGY
Representative

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Components

#1: Protein PIWI-LIKE PROTEIN 1 / MIWI


Mass: 17641.062 Da / Num. of mol.: 1 / Fragment: PAZ-DOMAIN, RESIDUES 276-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9JMB7
#2: RNA chain 5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3' / PIRNA


Mass: 2500.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BASED ON BIOLOGICAL SEQUENCE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
121NOESY
131EDITED -FILTERED
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.8 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NMRViewstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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