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- PDB-4n41: Structure of Thermus thermophilus Argonaute bound to guide DNA an... -

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Basic information

Entry
Database: PDB / ID: 4n41
TitleStructure of Thermus thermophilus Argonaute bound to guide DNA and 15-mer target DNA
Components
  • 5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3'
  • 5'-D(P*AP*CP*CP*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*T*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 / Argonaute, N-terminal domain / Argonaute, middle domain / Piwi domain profile. / Piwi domain ...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 / 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 / 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
DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.248 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 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / 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_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*T*GP*TP*AP*TP*AP*GP*T)-3'
E: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3'
D: 5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
F: 5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,7639
Polymers174,6906
Non-polymers733
Water3,063170
1
A: Argonaute
C: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3'
D: 5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2134
Polymers87,1893
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-48 kcal/mol
Surface area31380 Å2
MethodPISA
2
B: Argonaute
E: 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*T*GP*TP*AP*TP*AP*GP*T)-3'
F: 5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5505
Polymers87,5023
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-62 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.513, 101.699, 153.019
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
12chain C and segid C
22chain D and segid D
32chain E and segid E
42chain F and segid F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
112chain C and segid CC0
212chain D and segid DD0
312chain E and segid EE0
412chain F and segid FF0

NCS ensembles :
ID
1
2

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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, 4 molecules CEDF

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


Mass: 3871.538 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3'


Mass: 4184.745 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 2 types, 173 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.2 M sodium chloride, 0.1 M Tris-HCl, pH 8.5, 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: 2.248→50 Å / Num. obs: 86435 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 49.72 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.442 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.248-2.36.90.77257270.842198.9
2.3-2.367.40.66257450.8551100
2.36-2.427.50.57657140.8951100
2.42-2.57.50.48757490.9391100
2.5-2.587.50.39157570.9761100
2.58-2.677.50.30957191.0721100
2.67-2.777.50.23757531.2281100
2.77-2.97.50.19157571.3031100
2.9-3.057.50.14257431.4541100
3.05-3.247.50.10857771.6471100
3.24-3.57.50.0857901.881100
3.5-3.857.40.06357462.0861100
3.85-4.47.20.05657922.519199.9
4.4-5.557.10.04758182.316199.9
5.55-507.10.03258481.655198.9

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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
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F73

3f73


Resolution: 2.248→45.524 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.7809 / SU ML: 0.29 / σ(F): 1.33 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 4330 5.01 %
Rwork0.2229 --
obs0.2248 86385 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.48 Å2 / Biso mean: 68.4624 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.248→45.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10062 1189 3 170 11424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111689
X-RAY DIFFRACTIONf_angle_d1.27416151
X-RAY DIFFRACTIONf_chiral_restr0.061793
X-RAY DIFFRACTIONf_plane_restr0.0061899
X-RAY DIFFRACTIONf_dihedral_angle_d15.5644321
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5333X-RAY DIFFRACTION10.428TORSIONAL
12B5333X-RAY DIFFRACTION10.428TORSIONAL
21C504X-RAY DIFFRACTION10.428TORSIONAL
22D504X-RAY DIFFRACTION10.428TORSIONAL
23E504X-RAY DIFFRACTION10.428TORSIONAL
24F504X-RAY DIFFRACTION10.428TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.248-2.27360.32731410.28032622276395
2.2736-2.30040.30911520.266127222874100
2.3004-2.32840.27951280.257227212849100
2.3284-2.35790.30071490.252727612910100
2.3579-2.38890.30031360.25827262862100
2.3889-2.42160.311470.264126882835100
2.4216-2.45620.34511540.265927372891100
2.4562-2.49290.36251500.259727202870100
2.4929-2.53180.31111480.249526952843100
2.5318-2.57330.3031370.246727922929100
2.5733-2.61770.2781530.250627132866100
2.6177-2.66530.35371250.253927322857100
2.6653-2.71660.33411330.248127622895100
2.7166-2.7720.28471550.240326872842100
2.772-2.83230.33891360.239427952931100
2.8323-2.89810.26161540.236626902844100
2.8981-2.97060.27371440.242127602904100
2.9706-3.05090.30951520.244926912843100
3.0509-3.14070.26251390.25927632902100
3.1407-3.2420.311340.255727422876100
3.242-3.35790.3081280.238827562884100
3.3579-3.49230.26621260.244827892915100
3.4923-3.65110.28421300.225327402870100
3.6511-3.84350.25361530.218427262879100
3.8435-4.08420.24731500.217527602910100
4.0842-4.39930.2161700.189127142884100
4.3993-4.84160.20621350.19327602895100
4.8416-5.54110.23461470.203327732920100
5.5411-6.97720.26011680.2227622930100
6.9772-45.53370.20931560.1932756291298

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