PDB-3hm9: Crystal structure of T. thermophilus Argonaute complexed with DNA...

ID or keywords:

Entry

Database: PDB / ID: 3hm9

Title

Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand

Components

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'
5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'
Argonaute

Keywords

Nucleic Acid Binding Protein/DNA/RNA / argonaute / protein-DNA-RNA complex / Nucleic Acid Binding Protein-DNA-RNA 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

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Wang, Y. / Li, H. / Sheng, G. / Patel, D.J.

Citation

Journal: Nature / Year: 2009
Title: Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes.
Authors: Wang, Y. / Juranek, S. / Li, H. / Sheng, G. / Wardle, G.S. / Tuschl, T. / Patel, D.J.

History

Deposition	May 28, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Feb 21, 2024	Group: 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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hm9.cif.gz	152.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3hm9.ent.gz	111.4 KB	Display	PDB format
PDBx/mmJSON format	3hm9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/3hm9 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/3hm9	HTTPS FTP

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Related structure data

Related structure data	3hjfC 3hk2C 3ho1C 3hvrC 3hxmC 3dlb 3dlh 3f73 3hge PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4nca-2 5kdo-d 5i8q-1 2xgt-d 6bkf-d 4xx0-d 6qub-2 1eud-d 5jzg-d 1qju-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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PDB pages	PDBj / wwPDB / NCBI
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Deposited unit

A: Argonaute

X: 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'

Y: 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'

hetero molecules

89.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	111.916, 111.916, 175.551
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Argonaute Mass: 76728.734 Da / Num. of mol.: 1 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	5'-D(PTPGPAPGPGPTPAPGPTPAPGPGPTPTPGPTPAPTPAPGPT)-3' Mass: 6588.266 Da / Num. of mol.: 1 / Source method*: obtained synthetically
#3: RNA chain	5'-R(UPAPUPAPCPAPAPCPCPUPAPCPUPAPCPCPUPCPG)-3' Mass: 5942.584 Da / Num. of mol.: 1 / Source method*: obtained synthetically
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.05 %
Crystal grow	Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM MgCl2, 1.0 M Na tartrate, 50 mM Tris.HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 308 K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. obs: 17434 / % possible obs: 99.5 % / Observed criterion σ(F): -1 / Redundancy: 7.3 % / R_merge(I) obs: 0.06 / Net I/σ(I): 26.3
Reflection shell	Resolution: 3.3→3.38 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.444 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1128 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0088	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 60.16 / SU ML: 0.466 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.289	871	5 %	RANDOM
R_work	0.237	-	-	-
obs	0.239	17255	99.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 77.24 Å² / B_iso mean: 58.365 Å² / B_iso min: 20 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.17 Å²	0 Å²	0 Å²
2-	-	0.17 Å²	0 Å²
3-	-	-	-0.35 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4631	606	2	0	5239

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	5421
X-RAY DIFFRACTION	r_angle_refined_deg	1.398	2.105	7510
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.18	5	649
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.407	21.294	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.484	15	627
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.327	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	866
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3970
X-RAY DIFFRACTION	r_mcbond_it	0.32	1.5	3247
X-RAY DIFFRACTION	r_mcangle_it	0.645	2	5003
X-RAY DIFFRACTION	r_scbond_it	1.036	3	2174
X-RAY DIFFRACTION	r_scangle_it	1.746	4.5	2507

LS refinement shell

Resolution: 3.3→3.383 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.395	65	-
R_work	0.281	1161	-
all	-	1226	-
obs	-	-	100 %

Refinement TLS params.

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

ID	L11 (°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)
1	2.1654	-2.0858	-0.6444	4.6375	0.6222	0.2793	-0.5221	-0.7231	0.9153	1.2981	0.6524	-0.2157	0.1795	0.4573	-0.1303	0.9757	0.123	-0.2353	1.3049	-0.0607	0.9642	-27.5087	36.3535	15.7265
2	1.6027	-1.0922	-2.233	4.752	-3.6789	10.708	-0.3441	0.1211	-0.0303	0.0827	0.4395	0.7215	0.6467	-1.2636	-0.0954	0.2831	0.1028	-0.0365	1.0326	-0.0749	0.8915	-34.5187	18.4727	12.2599
3	1.4385	1.2719	-1.1848	1.2137	-1.0232	1.0047	0.0337	1.1745	0.3104	0.6511	0.5897	0.3991	-0.0478	-0.9217	-0.6233	2.2491	-0.3306	0.4248	2.7312	-0.3869	1.999	-47.4484	13.4705	39.6774
4	3.6551	-2.3547	1.182	3.6171	-1.7463	1.5392	0.0388	0.5608	-0.1284	-0.6644	0.058	0.5477	0.7735	-0.2409	-0.0968	0.6983	-0.0954	0.0224	1.0234	-0.0707	0.4931	-21.5284	9.9668	4.9847
5	1.8489	1.6143	-0.2864	4.5555	-1.5815	3.3111	-0.1765	0.3695	-0.4227	-0.3518	0.1241	-0.3337	0.6434	-0.0077	0.0524	0.3509	0.1549	0.1219	0.2596	-0.0635	0.4527	-8.2283	-9.5014	32.1802
6	1.4761	0.5358	-0.5396	2.9772	-0.3967	4.5856	-0.027	0.599	-0.1923	-0.3484	0.047	-0.1283	0.0813	0.0097	-0.0199	0.209	0.1405	0.1375	0.3678	-0.0009	0.2884	-4.988	8.4284	21.1011
7	6.7644	-2.7385	1.1889	3.3307	-3.4116	4.2813	-0.3948	0.4816	0.5282	-0.1349	0.752	0.4012	0.3979	-1.2688	-0.3572	0.505	-0.0078	-0.0234	0.6931	0.0572	0.7606	-23.8775	-0.1975	21.0311
8	17.1831	-2.2448	-0.0763	0.7845	1.144	2.7196	-0.2	0.3884	1.4018	-0.0657	-0.3367	0.1577	-0.1795	-0.704	0.5367	0.6867	0.2346	0.0358	0.7543	-0.0065	0.9597	-22.2257	21.2459	29.9138
9	12.6402	0.1798	-10.3522	2.559	5.6279	21.6588	-0.5166	1.2305	1.3857	-0.6907	0.0323	0.8447	-1.183	-0.6883	0.4844	0.5028	-0.0869	-0.1756	0.8734	-0.0767	0.8128	-20.1391	18.1185	23.733
10	6.278	-2.7748	3.2457	5.4275	4.5774	10.7256	0.4313	0.1867	-0.2194	-0.1093	-0.7666	0.6882	0.643	-1.3376	0.3352	0.8916	-0.3046	-0.0142	0.9562	0.1351	0.6261	-27.8356	-1.7407	20.6488

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 135
2	X-RAY DIFFRACTION	2	A	136 - 180
3	X-RAY DIFFRACTION	3	A	181 - 262
4	X-RAY DIFFRACTION	4	A	263 - 330
5	X-RAY DIFFRACTION	5	A	331 - 521
6	X-RAY DIFFRACTION	6	A	522 - 685
7	X-RAY DIFFRACTION	7	X	1 - 9
8	X-RAY DIFFRACTION	8	X	10 - 16
9	X-RAY DIFFRACTION	9	Y	6 - 10
10	X-RAY DIFFRACTION	10	Y	11 - 18

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