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

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Basic information

Entry
Database: PDB / ID: 4ncb
TitleStructure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+
Components
  • 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'
  • 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-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 / 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. / PAZ domain ...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. / 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
THYMIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 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 1.2Jun 8, 2016Group: Atomic model
Revision 1.3Sep 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 / software / 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_alt_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_alt_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 / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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'
P: 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'
D: 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*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'
H: 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,48116
Polymers180,6908
Non-polymers7908
Water7,999444
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'
P: 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'
D: 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1058
Polymers91,7104
Non-polymers3954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3768
Polymers88,9814
Non-polymers3954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.736, 105.363, 92.058
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211

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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 , 4 types, 6 molecules CEPHDF

#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(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'


Mass: 2683.801 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: obtained synthetically
#4: DNA chain 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'


Mass: 5708.726 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: obtained synthetically
#5: DNA chain 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'


Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 452 molecules

#6: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsHALF (OCCUPANCY = 0.50) OF CHAIN D PRESENT IN THE CRYSTAL HAS BEEN CLEAVED TO FORM CHAIN P AND ...HALF (OCCUPANCY = 0.50) OF CHAIN D PRESENT IN THE CRYSTAL HAS BEEN CLEAVED TO FORM CHAIN P AND CONFORMATION B OF CHAIN D.

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18 mM magnesium chloride, 9% isopropanol, 50 mM sodium cacodylate, pH 6.5, 2.25 mM spermine, 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: 2.189→50 Å / Num. obs: 75224 / % possible obs: 91.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.073 / Χ2: 0.993 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.189-2.242.40.45536660.714188.6
2.24-2.282.40.43336250.857189.1
2.28-2.322.40.36836500.646189.2
2.32-2.372.50.3537090.673189.8
2.37-2.422.50.31436840.664189.5
2.42-2.482.50.27936420.65189.3
2.48-2.542.50.25436440.645188.6
2.54-2.612.60.21336680.626189.3
2.61-2.692.60.19836270.68188.4
2.69-2.772.60.16736750.65189.4
2.77-2.872.70.14337210.638189.7
2.87-2.992.80.1236690.644189.4
2.99-3.122.80.10436800.665189.3
3.12-3.292.90.08337210.716190.2
3.29-3.4930.07237730.76191.4
3.49-3.7630.06538790.942194.2
3.76-4.142.90.05339091.069194.7
4.14-4.7430.04439941.199196.2
4.74-5.973.50.04341301.667199.3
5.97-503.50.03741582.773197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HM9

3hm9


Resolution: 2.189→39.216 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.8344 / SU ML: 0.29 / σ(F): 1.4 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 3787 5.04 %RANDOM
Rwork0.1748 ---
obs0.1776 75196 90.6 %-
all-75196 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.58 Å2 / Biso mean: 35.5953 Å2 / Biso min: 5.98 Å2
Refinement stepCycle: LAST / Resolution: 2.189→39.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10515 1417 48 444 12424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912451
X-RAY DIFFRACTIONf_angle_d1.11517248
X-RAY DIFFRACTIONf_chiral_restr0.0691889
X-RAY DIFFRACTIONf_plane_restr0.0041982
X-RAY DIFFRACTIONf_dihedral_angle_d18.5364725
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 (%)
2.189-2.21710.31161220.26832113223574
2.2171-2.24630.33351240.25562598272289
2.2463-2.27710.3191350.25142541267688
2.2771-2.30960.28971240.23632620274489
2.3096-2.34410.31251390.23142611275090
2.3441-2.38070.26961460.22472608275490
2.3807-2.41970.33061320.22522622275489
2.4197-2.46150.24711320.22462612274490
2.4615-2.50620.32221480.22092541268988
2.5062-2.55440.29751480.2142625277389
2.5544-2.60650.25171320.20452538267089
2.6065-2.66320.30321410.2062584272588
2.6632-2.72510.25591410.20752580272189
2.7251-2.79330.28051460.21152634278090
2.7933-2.86880.29541380.21492609274789
2.8688-2.95320.30081470.21722578272589
2.9532-3.04840.31321140.21552627274189
3.0484-3.15730.27541600.19422608276889
3.1573-3.28370.24541340.17592651278591
3.2837-3.43310.22791350.17482661279691
3.4331-3.61390.20231390.15612683282292
3.6139-3.84020.19931340.15492840297496
3.8402-4.13640.22211530.14472736288994
4.1364-4.55210.17461520.12622850300297
4.5521-5.20950.15571470.12592876302397
5.2095-6.55840.19171520.149729603112100
6.5584-39.22190.14951720.14092903307597
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.43580.4509-0.64320.7564-0.42991.40520.0796-0.21890.28030.23810.03280.1114-0.2410.2169-0.08790.2311-0.0503-0.01810.2558-0.0440.2146-16.47427.183844.0457
21.092-0.21540.23110.446-0.19320.486-0.0758-0.0508-0.01530.08230.034-0.17240.146-0.01090.03410.3791-0.0507-0.00890.2273-0.02070.26272.0193-6.77843.564
31.90440.5464-0.20450.6825-0.03070.414-0.16520.0661-0.0321-0.08180.1369-0.08980.08910.07940.02220.27210.00820.02490.1943-0.05680.154227.301714.73628.7757
40.99640.0951-0.21360.78380.38631.6963-0.07810.04370.0757-0.0410.03710.05650.0358-0.11470.03390.17320.0069-0.00640.1564-0.00070.142214.620124.953235.4181
51.62110.50331.11532.10670.3273.060.2490.1587-0.4724-0.2690.08550.1240.7819-0.3942-0.34220.4838-0.0368-0.06270.2844-0.01410.289515.4054-13.50181.3436
62.5005-2.49750.45366.47670.4181.39660.15540.02140.0354-0.2214-0.18290.13650.2094-0.1870.06340.1508-0.0515-0.00530.237-0.02440.085314.05213.920691.5738
72.49661.06922.38831.77580.71752.395-0.111300.3541-0.2667-0.22190.4962-0.2029-1.17690.30230.34510.1021-0.09090.7171-0.08120.3914-6.822321.812376.0672
82.8987-0.66712.10030.874-0.51683.3821-0.26160.03560.08860.04720.02640.2558-0.3509-0.57450.15890.22360.00620.0240.3521-0.08930.24093.594816.42985.8716
90.86760.1670.47661.5778-0.49460.9283-0.13120.15080.22040.1457-0.1241-0.2088-0.21890.23930.25140.15830.01010.00840.1334-0.01980.121934.15638.426772.1331
100.4657-0.2520.43411.7126-0.3032.11020.07960.1116-0.0424-0.1519-0.1071-0.07860.28620.1720.00970.11210.02030.02750.1453-0.01570.140133.465122.089370.2237
111.636-0.0124-0.64251.7327-0.18662.76160.0414-0.13930.16770.48420.06250.25010.3911-0.4405-0.14060.2827-0.09340.06050.3274-0.01420.262710.95897.941737.4766
123.1708-3.29060.5715.41072.23684.11860.3539-1.1871-0.94410.6046-0.20411.49861.3924-2.8351-0.09520.5789-0.3256-0.07371.5250.05820.5359-0.883710.158342.7738
131.4022-0.31731.39312.98920.51551.6145-0.1921-0.1937-0.11230.39260.10570.29410.2398-0.45030.09640.254-0.02170.10770.32640.02310.203115.1147.36930.796
142.84770.592-0.62732.4971-1.11110.6602-0.11040.0337-0.3477-0.13160.0197-0.0858-0.0607-0.1710.05350.0993-0.01290.03110.1284-0.03030.1219.377723.258481.3544
151.74220.2208-1.16462.617-2.43544.40.48590.3065-0.7342-1.115-1.3517-0.27690.9188-0.37940.61470.8509-0.02750.06780.3798-0.16990.664618.45842.493169.1671
161.05790.1094-0.54820.3670.20830.48080.46350.2886-2.1743-0.1076-0.3428-1.59831.54481.4623-0.10071.40110.4201-0.54151.11790.09682.073325.9103-12.670971.9915
172.70111.61530.75451.48961.29391.40060.008-0.11610.13460.0729-0.14080.0636-0.2164-0.14730.17310.33830.01990.0060.1465-0.01530.200421.332827.800382.6718
189.69014.71042.36986.91582.18892.5290.3923-1.016-0.90730.7254-0.0894-0.32090.9531-0.6793-0.32920.8185-0.1732-0.0770.41620.01850.450817.88311.927976.4575
194.3367-1.61545.57414.7729-0.37157.872-0.0233-0.17380.08630.44350.202-0.10470.0459-0.0171-0.12180.6165-0.04750.03390.5971-0.06080.498413.7337-13.271158.1443
201.106-2.76450.39549.63212.04288.41490.04440.6016-0.2252-0.6268-0.09580.37580.1117-0.4446-0.01140.2926-0.13580.10660.8717-0.2240.3227-8.849414.4967.4139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 72 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 263 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 443 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 444 through 685 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 102 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 174 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 222 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 223 through 301 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 302 through 400 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 401 through 685 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 16 )C0
12X-RAY DIFFRACTION12chain 'P' and (resid 5 through 9 )P0
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 19 )D0
14X-RAY DIFFRACTION14chain 'E' and (resid 2 through 11 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 12 through 16 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 17 through 17 )E0
17X-RAY DIFFRACTION17chain 'F' and (resid 10 through 19 )F0
18X-RAY DIFFRACTION18chain 'H' and (resid 4 through 9 )H0
19X-RAY DIFFRACTION19chain 'A' and (resid 701 through 701 )A0
20X-RAY DIFFRACTION20chain 'B' and (resid 701 through 701 )B0

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