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- PDB-3f73: Alignment of guide-target seed duplex within an argonaute silenci... -

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Basic information

Entry
Database: PDB / ID: 3f73
TitleAlignment of guide-target seed duplex within an argonaute silencing complex
Components
  • ARGONAUTE
  • DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3')
  • RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')
KeywordsNUCLEIC ACID BINDING PROTEIN/DNA/RNA / argonaute / protein-DNA-RNA-complex / NUCLEIC ACID BINDING PROTEIN-DNA-RNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding
Similarity search - Function
paz domain - #50 / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / paz domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi ...paz domain - #50 / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / paz domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / PAZ domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Response regulator / Beta Complex / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsWang, Y. / Li, H. / Sheng, G. / Juranek, S. / Tuschl, T. / Patel, D.J.
CitationJournal: Nature / Year: 2008
Title: Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex.
Authors: Wang, Y. / Juranek, S. / Li, H. / Sheng, G. / Tuschl, T. / Patel, D.J.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGONAUTE
B: ARGONAUTE
C: DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3')
H: RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')
X: DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3')
Y: RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,29910
Polymers179,1326
Non-polymers1684
Water28816
1
A: ARGONAUTE
C: DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3')
H: RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7096
Polymers89,5663
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-67 kcal/mol
Surface area31740 Å2
MethodPISA
2
B: ARGONAUTE
X: DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3')
Y: RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5904
Polymers89,5663
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-50 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.162, 120.527, 109.085
Angle α, β, γ (deg.)90.00, 105.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain / RNA chain , 3 types, 6 molecules ABCXHY

#1: Protein ARGONAUTE


Mass: 76728.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_P0026 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q746M7
#2: DNA chain DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3')


Mass: 6588.266 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')


Mass: 6248.750 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 20 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.16 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 308 K / pH: 5.6
Details: 10% (v/v) PEG400, 50mM Mes 5.6, 0.1M KCl, 15 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 308K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2MES11
3KCL11
4MgCl211
5PEG 40012
6MES12
7KCl12
8MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 29830 / Redundancy: 4.2 % / Rsym value: 0.081 / Net I/σ(I): 15.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.397 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementStarting model: PDB ENTRY 3DLH

3dlh


Resolution: 3→30 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2073 6.8 %RANDOM
Rwork0.221 ---
obs0.221 29792 97.3 %-
Solvent computationBsol: 36.88 Å2
Displacement parametersBiso mean: 70.28 Å2
Baniso -1Baniso -2Baniso -3
1--7.517 Å20 Å2-0.272 Å2
2--12.793 Å20 Å2
3----5.276 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10044 980 8 16 11048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å
RfactorNum. reflection% reflection
Rfree0.367 329 -
Rwork0.317 --
obs--95.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION5
X-RAY DIFFRACTION6

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