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- PDB-3dlh: Crystal structure of the guide-strand-containing Argonaute protei... -

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Basic information

Entry
Database: PDB / ID: 3dlh
TitleCrystal structure of the guide-strand-containing Argonaute protein silencing complex
Components
  • Argonaute
  • DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3')
KeywordsNucleic Acid Binding Protein/dna / argonaute / PROTEIN-DNA COMPLEX / Plasmid / Nucleic Acid Binding Protein-dna 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
ACETIC ACID / TRIETHYLENE GLYCOL / PHOSPHATE ION / DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsWang, Y. / Sheng, G. / Patel, D.J.
CitationJournal: Nature / Year: 2008
Title: Structure of the guide-strand-containing argonaute silencing complex.
Authors: Wang, Y. / Sheng, G. / Juranek, S. / Tuschl, T. / Patel, D.J.
History
DepositionJun 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
X: DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3')
Y: DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,16712
Polymers166,6344
Non-polymers5338
Water1,35175
1
A: Argonaute
X: DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7067
Polymers83,3172
Non-polymers3895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-48 kcal/mol
Surface area32020 Å2
MethodPISA
2
B: Argonaute
Y: DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4615
Polymers83,3172
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-36 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.744, 114.629, 175.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABXY

#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 DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3')


Mass: 6588.266 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 5 types, 83 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG8000, 200mM KCl, 80mM MgAc2, 50mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 308K
Components of the solutions
IDNameCrystal-IDSol-ID
1Mes11
2Mes12
3KCl12
4MgAc212
5PEG800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30932 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2 / Num. unique all: 2926 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3→30 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.284 2037 6.6 %
Rwork0.226 --
obs-28771 93 %
Solvent computationBsol: 29.252 Å2
Displacement parametersBiso max: 151.86 Å2 / Biso mean: 58.357 Å2 / Biso min: 11.27 Å2
Baniso -1Baniso -2Baniso -3
1--6.191 Å20 Å20 Å2
2--8.963 Å20 Å2
3----2.772 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 588 23 83 10986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.634
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:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5acy_xplor_par.param

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