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- PDB-3mj0: Crystal Structure of Drosophia Ago-PAZ domain in complex with 3'-... -

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Basic information

Entry
Database: PDB / ID: 3mj0
TitleCrystal Structure of Drosophia Ago-PAZ domain in complex with 3'-end 2'-O-methylated RNA
Components
  • Protein argonaute-2
  • RNA (5'-R(*CP*GP*UP*UP*AP*CP*GP*CP*(OMU))-3')
KeywordsRNA/RNA BINDING PROTEIN / Argonaut / PAZ domain / 3'-end 2'-O-methylated ssRNA / RNA-RNA BINDING PROTEIN complex
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 / Transcriptional regulation by small RNAs ...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 / 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 / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA binding / siRNA processing / 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 / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
paz domain / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 ...paz domain / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / 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 profile. / PAZ domain / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / Protein argonaute-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsHuang, Y. / Ding, L. / Ma, J.
CitationJournal: To be Published
Title: Crystal Structure of drosophila Ago2 PAZ domain in complex with 3'-end 2'-O-methylated RNA
Authors: Huang, Y. / Ding, L. / Ma, J.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute-2
B: RNA (5'-R(*CP*GP*UP*UP*AP*CP*GP*CP*(OMU))-3')


Theoretical massNumber of molelcules
Total (without water)16,9802
Polymers16,9802
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.211, 116.796, 38.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein argonaute-2


Mass: 14157.182 Da / Num. of mol.: 1 / Fragment: UNP residues 601-723, PAZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: AGO2, CG7439 / Plasmid: pET28-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q9VUQ5
#2: RNA chain RNA (5'-R(*CP*GP*UP*UP*AP*CP*GP*CP*(OMU))-3')


Mass: 2822.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50 mM MES, pH 5.8, 100 mM ammonium sulfate, 10 mM MgCl2, 16% PEG 8000 and 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2008
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 7212 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 35.04
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 5.578 / Rsym value: 0.327 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R6Z

1r6z


Resolution: 2.306→25.785 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 30.94 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2743 337 4.68 %
Rwork0.2218 --
obs0.2244 7202 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.515 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4547 Å20 Å2-0 Å2
2--0.0596 Å20 Å2
3----0.5143 Å2
Refinement stepCycle: LAST / Resolution: 2.306→25.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 186 0 33 1170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111182
X-RAY DIFFRACTIONf_angle_d1.5021609
X-RAY DIFFRACTIONf_dihedral_angle_d19.807445
X-RAY DIFFRACTIONf_chiral_restr0.074184
X-RAY DIFFRACTIONf_plane_restr0.009179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.306-2.90470.34161650.27583364X-RAY DIFFRACTION100
2.9047-25.78640.2551720.20623501X-RAY DIFFRACTION100

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