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- PDB-3hvr: Crystal structure of T. thermophilus Argonaute complexed with DNA... -

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Basic information

Entry
Database: PDB / ID: 3hvr
TitleCrystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site
Components
  • 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3'
  • 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
  • Argonaute
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 / Argonaute, N-terminal domain / Argonaute, middle domain / paz domain ...paz domain - #50 / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / paz domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain profile. / PAZ domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / 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 / MOLECULAR REPLACEMENT / Resolution: 3.211 Å
AuthorsWang, Y. / Li, H. / Sheng, G. / Patel, D.J.
CitationJournal: Nature / Year: 2009
Title: Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes.
Authors: Wang, Y. / Juranek, S. / Li, H. / Sheng, G. / Wardle, G.S. / Tuschl, T. / Patel, D.J.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: 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: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3'
M: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3'
D: 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
N: 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,85514
Polymers178,5196
Non-polymers3368
Water00
1
A: Argonaute
C: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3'
D: 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4277
Polymers89,2603
Non-polymers1684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-75 kcal/mol
Surface area32730 Å2
MethodPISA
2
B: Argonaute
M: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3'
N: 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4277
Polymers89,2603
Non-polymers1684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-69 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.252, 116.903, 170.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / Plasmid: PET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3)pLysS / References: UniProt: Q746M7
#2: DNA chain 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3'


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


Mass: 5942.584 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 80 mM MgCl2, 1.0 M Na tartrate, 50 mM Tris.HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 308 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 34970 / % possible obs: 95.2 % / Observed criterion σ(F): -1 / Redundancy: 4.9 % / Biso Wilson estimate: 95.75 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3220 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HK2

3hk2


Resolution: 3.211→37.68 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU ML: 0.51 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1743 4.99 %RANDOM
Rwork0.226 ---
obs0.229 34940 94.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.32 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 293.57 Å2 / Biso mean: 97.522 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.626 Å20 Å20 Å2
2--8.149 Å2-0 Å2
3----11.775 Å2
Refinement stepCycle: LAST / Resolution: 3.211→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9513 1108 16 0 10637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810997
X-RAY DIFFRACTIONf_angle_d1.11115215
X-RAY DIFFRACTIONf_chiral_restr0.0711729
X-RAY DIFFRACTIONf_plane_restr0.0081807
X-RAY DIFFRACTIONf_dihedral_angle_d16.2163925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.211-3.3060.4141280.3432257238578
3.306-3.4120.3761540.2982620277491
3.412-3.5340.3461170.2622701281893
3.534-3.6750.281310.2342712284394
3.675-3.8420.3021530.2092769292295
3.842-4.0450.2781330.1992768290195
4.045-4.2980.2441400.1932812295297
4.298-4.6290.2371580.1732860301898
4.629-5.0940.2431640.1832843300798
5.094-5.8290.2541620.1952891305398
5.829-7.3350.241500.2162949309999
7.335-37.6830.2381530.2193015316897

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