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- PDB-4n76: Structure of Thermus thermophilus Argonaute bound to guide DNA an... -

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Basic information

Entry
Database: PDB / ID: 4n76
TitleStructure of Thermus thermophilus Argonaute bound to guide DNA and cleaved target DNA with Mn2+
Components
  • 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 / Piwi / 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: 2.89 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 15, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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'
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'
D: 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
F: 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,13611
Polymers172,5946
Non-polymers5425
Water48627
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3524
Polymers86,2973
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-31 kcal/mol
Surface area29920 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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7847
Polymers86,2973
Non-polymers4874
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-47 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.918, 117.420, 160.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 11:21 or resseq 316:354 or resseq...
21chain B and (resseq 11:21 or resseq 316:354 or resseq...
12chain C and (resseq 1:10 )
22chain E and (resseq 1:10 )
13chain D and (resseq 11:19 )
23chain F and (resseq 11:19 )

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUPROPROchain A and (resseq 11:21 or resseq 316:354 or resseq...AA11 - 2111 - 21
121LEULEUALAALAchain A and (resseq 11:21 or resseq 316:354 or resseq...AA316 - 354316 - 354
131GLYGLYASNASNchain A and (resseq 11:21 or resseq 316:354 or resseq...AA388 - 436388 - 436
141PHEPHEGLUGLUchain A and (resseq 11:21 or resseq 316:354 or resseq...AA485 - 512485 - 512
151ALAALAARGARGchain A and (resseq 11:21 or resseq 316:354 or resseq...AA534 - 608534 - 608
161GLYGLYASPASPchain A and (resseq 11:21 or resseq 316:354 or resseq...AA612 - 660612 - 660
171LEULEUVALVALchain A and (resseq 11:21 or resseq 316:354 or resseq...AA662 - 685662 - 685
211LEULEUPROPROchain B and (resseq 11:21 or resseq 316:354 or resseq...BB11 - 2111 - 21
221LEULEUALAALAchain B and (resseq 11:21 or resseq 316:354 or resseq...BB316 - 354316 - 354
231GLYGLYASNASNchain B and (resseq 11:21 or resseq 316:354 or resseq...BB388 - 436388 - 436
241PHEPHEGLUGLUchain B and (resseq 11:21 or resseq 316:354 or resseq...BB485 - 512485 - 512
251ALAALAARGARGchain B and (resseq 11:21 or resseq 316:354 or resseq...BB534 - 608534 - 608
261GLYGLYASPASPchain B and (resseq 11:21 or resseq 316:354 or resseq...BB612 - 660612 - 660
271LEULEUVALVALchain B and (resseq 11:21 or resseq 316:354 or resseq...BB662 - 685662 - 685
112DTDTDADAchain C and (resseq 1:10 )CC1 - 101 - 10
212DTDTDADAchain E and (resseq 1:10 )ED1 - 101 - 10
113DADADGDGchain D and (resseq 11:19 )DE11 - 192 - 10
213DADADGDGchain F and (resseq 11:19 )FF11 - 192 - 10

NCS ensembles :
ID
1
2
3

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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 , 2 types, 4 molecules CEDF

#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

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Non-polymers , 3 types, 32 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE / Thymidine monophosphate


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Comment: dTMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8 M sodium acetate, 0.1 M Bis-Tris propane, pH 6.8, 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: 2.89→50 Å / Num. all: 47634 / Num. obs: 45264 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 42.94 Å2 / Rmerge(I) obs: 0.16
Reflection shellResolution: 2.89→3 Å / % possible all: 82.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N47

4n47


Resolution: 2.89→49.372 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8106 / SU ML: 0.43 / σ(F): 1.39 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 2293 5.07 %RANDOM
Rwork0.219 ---
obs0.2215 45258 95.05 %-
all-45258 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.84 Å2 / Biso mean: 35.3682 Å2 / Biso min: 0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.89→49.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9918 848 25 27 10818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711167
X-RAY DIFFRACTIONf_angle_d1.10715361
X-RAY DIFFRACTIONf_chiral_restr0.0561708
X-RAY DIFFRACTIONf_plane_restr0.0041854
X-RAY DIFFRACTIONf_dihedral_angle_d16.9714106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2116X-RAY DIFFRACTIONPOSITIONAL0.015
12B2116X-RAY DIFFRACTIONPOSITIONAL0.015
21C211X-RAY DIFFRACTIONPOSITIONAL0.011
22E211X-RAY DIFFRACTIONPOSITIONAL0.011
31D180X-RAY DIFFRACTIONPOSITIONAL0.145
32F180X-RAY DIFFRACTIONPOSITIONAL0.145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.95290.3981080.34431952206070
2.9529-3.02160.3721390.33792469260889
3.0216-3.09710.37151320.31682590272292
3.0971-3.18090.33661310.27712607273894
3.1809-3.27440.30951440.25912672281696
3.2744-3.38010.30681460.24262667281396
3.3801-3.50090.27331560.21862701285796
3.5009-3.6410.2671640.20142684284897
3.641-3.80670.24721380.20482793293198
3.8067-4.00730.24131430.17782747289098
4.0073-4.25820.22171350.16492803293898
4.2582-4.58680.18761540.16032780293499
4.5868-5.0480.21681510.1662816296799
5.048-5.77740.25811320.19922841297399
5.7774-7.27520.2821570.23932855301299
7.2752-49.37910.27121630.23812988315199

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