PDB-5ux0: X-ray crystal structure of Marinitoga piezophila Argonaute in com...

ID or keywords:

Entry

Database: PDB / ID: 5ux0

Title

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA

Components

Argonaute protein
DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')
RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')

Keywords

HYDROLASE/RNA/DNA / Argonaute / RNAi / RNA / DNA / HYDROLASE-RNA-DNA complex

Function / homology

Function and homology information

Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / DNA endonuclease activity / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Marinitoga piezophila (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.197 Å

Authors

Doxzen, K.W. / Doudna, J.A.

Citation

Journal: PLoS ONE / Year: 2017
Title: DNA recognition by an RNA-guided bacterial Argonaute.
Authors: Doxzen, K.W. / Doudna, J.A.

History

Deposition	Feb 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2017	Group: Database references
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Dec 25, 2024	Group: Advisory / Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5ux0_validation.pdf.gz	477.2 KB	Display	wwPDB validaton report
Full document	5ux0_full_validation.pdf.gz	501.2 KB	Display
Data in XML	5ux0_validation.xml.gz	53.1 KB	Display
Data in CIF	5ux0_validation.cif.gz	69.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/5ux0 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5ux0	HTTPS FTP

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Related structure data

Related structure data	5i4aS S: Starting model for refinement
Similar structure data	2bu7-1 6chj-d 2nrc-1 2nrb-1 3d2r-d 3bvu-d 2id0-3 4mp2-1 2id0-2 1lkx-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Argonaute protein

B: RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')

C: DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')

D: Argonaute protein

E: RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')

F: DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')

179 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Argonaute protein

B: RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')

C: DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')

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

2

D: Argonaute protein

E: RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')

F: DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')

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

Unit cell

Length a, b, c (Å)	85.003, 130.993, 171.468
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain B and resseq 2:18)
2	1	(chain E and resseq 2:18)
1	2	(chain A and (resseq 1 or (resid 2 and (name...
2	2	(chain D and (resseq 1 or (resid 2 and (name...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain B and resseq 2:18)	B	2 - 18
2	1	1	(chain E and resseq 2:18)	E	2 - 18
1	1	2	(chain A and (resseq 1 or (resid 2 and (name...	A	0
2	1	2	(chain D and (resseq 1 or (resid 2 and (name...	D	0

NCS ensembles :

ID
1
2

#1: Protein	Argonaute protein Mass: 76146.234 Da / Num. of mol.: 2 / Mutation: D516A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinitoga piezophila (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2J4R4
#2: RNA chain	RNA (5'-R(GGPUPAPCPAPAPCPCPUPAPCPUPAPCPCPUPCPAPU)-3') Mass: 6593.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain	DNA (5'-D(PAPTPGPAPGPGPTPAPGPTPAPGPGPTPTPGPTPAPCPC)-3') Mass: 6542.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 27% PEG 4,000, 0.1M MES, 275 mM KI

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.11587 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.11587 Å / Relative weight: 1

Reflection

Resolution: 3.197→47.431 Å / Num. obs: 32393 / % possible obs: 99.7 % / Redundancy: 4.9 % / B_iso Wilson estimate: 74.34 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.152 / R_pim(I) all: 0.076 / R_rim(I) all: 0.17 / Net I/σ(I): 8.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
3.2-3.37	4.9	0.878	4583	0.677	0.443	0.986	98.3
10.11-47.43	4.5	0.027		0.999	0.014	0.03	99.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
Aimless	0.5.17	data scaling
PHASER		phasing
PHENIX	1.10_2155	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5I4A

5i4a

Resolution: 3.197→47.431 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27

	R_factor	Num. reflection	% reflection
R_free	0.2587	1616	5 %
R_work	0.2154	-	-
obs	0.2176	32316	99.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 220.77 Å² / B_iso mean: 81.3429 Å² / B_iso min: 12.33 Å²

Refinement step

Cycle: final / Resolution: 3.197→47.431 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10699	1538	0	0	12237
Num. residues	-	-	-	-	1345

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12680
X-RAY DIFFRACTION	f_angle_d	0.655	17436
X-RAY DIFFRACTION	f_chiral_restr	0.047	1922
X-RAY DIFFRACTION	f_plane_restr	0.006	1936
X-RAY DIFFRACTION	f_dihedral_angle_d	15.223	7420

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	B	402	X-RAY DIFFRACTION	10.167	TORSIONAL
1	2	E	402	X-RAY DIFFRACTION	10.167	TORSIONAL
2	1	A	4996	X-RAY DIFFRACTION	10.167	TORSIONAL
2	2	D	4996	X-RAY DIFFRACTION	10.167	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 12

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.1968-3.2908	0.3787	128	0.3274	2423	2551	97
3.2908-3.397	0.3638	134	0.2926	2547	2681	100
3.397-3.5184	0.3284	131	0.2789	2525	2656	100
3.5184-3.6592	0.3252	134	0.2501	2533	2667	100
3.6592-3.8257	0.2986	133	0.2332	2526	2659	100
3.8257-4.0273	0.2903	133	0.2235	2526	2659	100
4.0273-4.2795	0.2875	135	0.2052	2563	2698	100
4.2795-4.6096	0.251	134	0.1801	2539	2673	100
4.6096-5.073	0.2029	135	0.1736	2578	2713	100
5.073-5.806	0.2251	137	0.1902	2590	2727	100
5.806-7.3106	0.2593	137	0.2206	2606	2743	100
7.3106-47.436	0.2008	145	0.197	2744	2889	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	2.6646	0.6824	-1.6351	2.3247	-1.2607	2.8254	-0.2841	-0.4345	-0.5959	0.2815	-0.3059	-0.3357	0.3152	0.3106	-5.4092	0.3169	0.1948	-0.016	0.0498	-0.0474	0.1428	86.9666	116.8315	50.5196
2	1.7874	0.4157	-0.6303	2.3647	-0.8405	1.4722	0.0685	0.4231	0.5747	-0.2128	-0.1017	-0.3414	-0.2655	0.1778	-0.0626	0.4488	0.0498	-0.0077	0.5271	0.1139	0.5707	95.5689	144.0007	24.5495
3	1.9888	0.2077	-0.0248	1.3279	1.3751	1.4323	0.1886	0.6416	-0.5744	0.1287	1.2587	-0.2217	0.2125	0.8868	0.9881	0.6319	0.2183	0.2697	0.923	0.186	0.9127	100.4932	137.1742	19.2341
4	1.0342	0.1028	-0.6452	0.6253	0.0354	0.5028	0.7383	-1.7301	0.8557	1.3086	-0.2456	-0.5069	-0.9059	0.4166	0.0487	1.7772	-0.1792	-0.0046	1.6383	-0.0871	0.9633	99.6742	126.8346	48.9009
5	1.2387	-0.0089	-0.3959	0.1578	-0.0177	0.1122	0.3354	-1.4247	0.5079	0.587	-0.2812	-0.3226	-1.0243	0.3721	-0.0617	1.6979	-0.2374	0.1753	1.4404	0.0487	1.0426	101.7792	127.5095	46.6837
6	0.0389	0.0198	0.0558	0.226	-0.0519	0.0766	-0.5301	0.5003	0.5455	-0.8825	0.5156	0.5301	-0.173	-0.4464	-0.001	1.5421	0.3767	0.265	1.2	0.3404	0.8856	94.4627	129.0618	14.6759
7	1.3604	-0.8627	0.193	0.8746	0.8095	2.3641	0.0366	-0.3175	-0.2583	0.0337	-0.3139	0.1709	0.1833	-0.6333	0.0737	0.4995	-0.0346	-0.0238	0.4743	-0.0754	0.2557	59.9745	123.483	13.399
8	1.0735	-0.2881	0.2625	1.1125	0.3168	2.616	0.1303	0.3306	-0.1201	-0.0561	-0.1208	-0.0547	0.132	0.3992	0.0089	0.2178	0.0478	-0.0414	0.4641	0.0227	0.3103	76.0956	119.221	-20.6596
9	1.3221	0.0104	0.577	1.3519	-1.4926	2.5747	-0.2899	0.5387	0.7564	0.4166	0.389	-0.288	-1.1543	0.3249	0.1828	0.513	-0.0254	-0.022	0.9973	0.0031	0.2705	78.934	127.2485	-23.5297
10	0.9703	0.6556	-0.2577	2.1888	-0.2278	0.0739	-0.0514	0.5947	-0.0283	-0.5814	0.157	0.2475	0.7185	0.0509	0.2481	0.8838	0.1088	0.1232	0.8546	-0.1314	0.3775	68.1603	131.125	-8.5213
11	5.6673	1.475	5.1975	3.5263	2.7672	5.7659	1.2648	-1.4389	-0.432	1.5155	-0.6513	0.5578	1.424	-1.4382	0.054	1.554	-0.5853	-0.3142	1.9923	0.1178	1.3388	52.1455	121.0222	-8.1536
12	5.9281	0.7563	-2.8768	2.2246	-0.6037	3.4041	-0.6131	-0.0712	-0.5196	0.3509	0.5878	0.0076	0.8986	-1.6383	0.2268	2.1685	-0.3973	0.2545	1.8191	-0.2668	1.5648	44.573	115.9498	4.4364
13	5.9723	-1.6752	4.5762	6.8918	-2.6991	4.2466	0.6952	-0.5	-0.0585	2.0357	0.1048	0.9603	-0.16	-2.0042	-0.1807	1.8669	0.1785	0.5302	1.5647	-0.0467	1.9315	54.3147	121.2287	0.5799
14	0.4703	-0.5327	-0.1476	0.6211	0.6663	0.3927	-0.777	1.7467	-1.4999	0.6173	0.296	0.4054	0.8525	-0.4306	-0.0005	1.262	-0.0414	0.2524	1.4231	-0.1263	0.8917	73.4955	130.5287	-15.6865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 197 )	A	0 - 197
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 198 through 639 )	A	198 - 639
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 5 )	B	1 - 5
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 6 through 20 )	B	6 - 20
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 2 through 16 )	C	2 - 16
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 17 through 21 )	C	17 - 21
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 1 through 165 )	D	1 - 165
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 166 through 639 )	D	166 - 639
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 1 through 5 )	E	1 - 5
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 6 through 10 )	E	6 - 10
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 11 through 15 )	E	11 - 15
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 16 through 18 )	E	16 - 18
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 6 through 10 )	F	6 - 10
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 11 through 21 )	F	11 - 21

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