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- PDB-4nca: Structure of Thermus thermophilus Argonaute bound to guide DNA 19... -

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Basic information

Entry
Database: PDB / ID: 4nca
TitleStructure of Thermus thermophilus Argonaute bound to guide DNA 19-mer and target DNA in the presence of Mg2+
Components
  • 5'-D(*AP*CP*AP*AP*CP*C)-3'
  • 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
  • 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
  • Argonaute
KeywordsNUCLEAR PROTEIN/DNA / Argonaute / RNA interference / DNA interference / NUCLEAR 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
Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 ...Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Response regulator / 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 / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.489 Å
AuthorsSheng, G. / Zhao, H. / Wang, J. / Rao, Y. / Wang, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Authors: Sheng, G. / Zhao, H. / Wang, J. / Rao, Y. / Tian, W. / Swarts, D.C. / van der Oost, J. / Patel, D.J. / Wang, Y.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _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
C: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
D: 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
E: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
F: 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
G: 5'-D(*AP*CP*AP*AP*CP*C)-3'
H: 5'-D(*AP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,90916
Polymers176,1188
Non-polymers7908
Water5,765320
1
A: Argonaute
C: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
D: 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
G: 5'-D(*AP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4548
Polymers88,0594
Non-polymers3954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-68 kcal/mol
Surface area30750 Å2
MethodPISA
2
B: Argonaute
E: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'
F: 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
H: 5'-D(*AP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4548
Polymers88,0594
Non-polymers3954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-74 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.950, 117.561, 160.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: Thermophilus / Gene: Argonaute, TT_P0026 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q746M7

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DNA chain , 3 types, 6 molecules CEDFGH

#2: DNA chain 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'


Mass: 6588.266 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'


Mass: 2979.968 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain 5'-D(*AP*CP*AP*AP*CP*C)-3'


Mass: 1762.208 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 328 molecules

#5: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE / Thymidine monophosphate


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P / Comment: dTMP*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.6 M sodium acetate, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 306K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.489→50 Å / Num. obs: 73777 / % possible obs: 99.9 % / Observed criterion σ(F): 2.07 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 46.62 Å2 / Rmerge(I) obs: 0.127 / Χ2: 0.872 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.489-2.5960.9272550.562199.5
2.59-2.6960.75572850.834199.9
2.69-2.826.40.57672990.615199.9
2.82-2.966.60.40972950.6341100
2.96-3.156.80.26673190.6361100
3.15-3.396.90.17473540.6571100
3.39-3.736.60.15373561.11199.9
3.73-4.276.90.09274030.954199.8
4.27-5.387.10.07274731.5041100
5.38-506.90.0477381.082199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.489→48.161 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8249 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 24.61 / Stereochemistry target values: ML / Details: PDB ENTRY 3F73
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 3714 5.04 %RANDOM
Rwork0.2003 ---
obs0.2026 73688 99.42 %-
all-73688 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.32 Å2 / Biso mean: 62.9704 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.489→48.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10627 1311 48 320 12306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112425
X-RAY DIFFRACTIONf_angle_d0.90617184
X-RAY DIFFRACTIONf_chiral_restr0.0341875
X-RAY DIFFRACTIONf_plane_restr0.0042002
X-RAY DIFFRACTIONf_dihedral_angle_d17.2894709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.489-2.52080.40251260.34072251237787
2.5208-2.55390.29571440.304325462690100
2.5539-2.58890.33311310.282725842715100
2.5889-2.62590.31321300.277525602690100
2.6259-2.66510.35671270.30225702697100
2.6651-2.70670.37931350.288225752710100
2.7067-2.75110.31411340.250325822716100
2.7511-2.79850.28931450.245125742719100
2.7985-2.84940.29691280.235526042732100
2.8494-2.90420.2821310.23325572688100
2.9042-2.96350.28431400.227126072747100
2.9635-3.02790.27271460.231825642710100
3.0279-3.09830.29811170.214126352752100
3.0983-3.17580.29261370.201725852722100
3.1758-3.26170.25031370.195925932730100
3.2617-3.35760.22571420.188926002742100
3.3576-3.4660.26431430.212125732716100
3.466-3.58980.24341340.189525982732100
3.5898-3.73350.24781430.212525872730100
3.7335-3.90330.23441450.199425952740100
3.9033-4.1090.21921640.173325792743100
4.109-4.36630.19461580.156726122770100
4.3663-4.70320.20411410.151326102751100
4.7032-5.1760.21541460.166326532799100
5.176-5.92380.25141340.191726592793100
5.9238-7.45890.2191280.199127062834100
7.4589-48.16980.1891280.17452815294399

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