PDB-4f1n: Crystal structure of Kluyveromyces polysporus Argonaute with a gu...

ID or keywords:

Entry

Database: PDB / ID: 4f1n

Title

Crystal structure of Kluyveromyces polysporus Argonaute with a guide RNA

Components

KpAGO
RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'

Keywords

RNA BINDING PROTEIN/RNA /

Argonaute /

RNAi /

RNAse H / RNA BINDING PROTEIN-RNA complex

Function / homology

Function and homology information

Biological species

Vanderwaltozyma polyspora (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.187 Å

Authors

Nakanishi, K. / Weinberg, D.E. / Bartel, D.P. / Patel, D.J.

Citation

Journal: Nature / Year: 2012
Title: Structure of yeast Argonaute with guide RNA.
Authors: Nakanishi, K. / Weinberg, D.E. / Bartel, D.P. / Patel, D.J.

History

Deposition	May 7, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 4, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4f1n.cif.gz	740.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4f1n.ent.gz	597.5 KB	Display	PDB format
PDBx/mmJSON format	4f1n.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/f1/4f1n ftp://data.pdbj.org/pub/pdb/validation_reports/f1/4f1n	HTTPS FTP

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Related structure data

Similar structure data	6kr4-2 3iay-d 5iud-4 4fyd-1 5iud-1 5gqh-d 2ox5-d 4s2r-d 1143 6z81-d 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
Related items in Molecule of the Month	#98 - Feb 2008 Small Interfering RNA similarity (8)

Deposited unit

A: KpAGO

E: RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'

B: KpAGO

F: RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'

241 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: KpAGO

E: RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'

defined by author&software
121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: KpAGO

F: RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'

defined by author&software
121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	171.553, 171.553, 83.177
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'A' and (resseq 221:282 )
2	1	1	chain 'B' and (resseq 221:282 )
1	1	2	chain 'A' and (resseq 302:350 )
2	1	2	chain 'B' and (resseq 302:350 )
1	1	3	chain 'A' and (resseq 388:542 )
2	1	3	chain 'B' and (resseq 388:542 )
1	1	4	chain 'A' and (resseq 659:709 )
2	1	4	chain 'B' and (resseq 659:709 )
1	1	5	chain 'A' and (resseq 722:837 )
2	1	5	chain 'B' and (resseq 721:836 )
1	1	6	chain 'A' and (resseq 865:1219 )
2	1	6	chain 'B' and (resseq 866:1219 )
1	1	7	chain 'A' and (resseq 1230:1251 )
2	1	7	chain 'B' and (resseq 1230:1251 )
1	1	8	chain 'E' and (resseq 1:9)
2	1	8	chain 'F' and (resseq 1:9)

NCS ensembles :

ID
1
2
3
4
5
6
7
8

#1: Protein	KpAGO Mass: 117800.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vanderwaltozyma polyspora (fungus) / Strain: ATCC 22028 / DSM 70294 / Gene: Kpol_520p25 / Production host: Escherichia coli (E. coli) / References: UniProt: A7TMA9
#2: RNA chain	RNA 5'-R(PUPAPAPAPAPAPAPAPA)-3' Mass: 2894.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vanderwaltozyma polyspora* (fungus) / Strain: ATCC 22028 / DSM 70294 / Gene: Kpol_520p25 / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
Source details	THE RNA WAS CO-PURIFIED WITH THE RECOMBINANT PROTEIN DURING THE OVEREXPRESSION IN E. COLI. OUR ...THE RNA WAS CO-PURIFIED WITH THE RECOMBINANT PROTEIN DURING THE OVEREXPRESSION IN E. COLI. OUR SEQUENCE ANALYSES FOR THE BOUND RNAS REVEALED THAT THEY ORIGINATED FROM MRNAS TRANSCRIBED FROM THE EXPRESSION VECTOR AND FROM E. COLI GENOME (THE STRAIN IS BL21(DE3)ROSETTA2)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 57.98 %
Crystal grow	Temperature: 293 K / Method: evaporation, recrystallization / pH: 5 Details: 100 mM MIB pH 5.0, 3% 1,4-dioxane, 19% PEG3350, 12 mM MnCl2, and 3% ethanol, EVAPORATION, RECRYSTALLIZATION, temperature 293K

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Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 3.187→50 Å / Num. obs: 45536 / % possible obs: 100 % / Redundancy: 5.8 % / R_merge(I) obs: 0.186 / Net I/σ(I): 12.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHELXS		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.187→38.119 Å / SU ML: 0.33 / σ(F): 1.96 / Phase error: 21.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2162	1994	4.39 %
R_work	0.1683	-	-
obs	0.1705	45435	99.52 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 19.409 Å² / k_sol: 0.309 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.0524 Å²	-0 Å²	-0 Å²
2-	-	-2.0524 Å²	0 Å²
3-	-	-	-2.7428 Å²

Refinement step

Cycle: LAST / Resolution: 3.187→38.119 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14034	358	0	34	14426

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	14742
X-RAY DIFFRACTION	f_angle_d	1.347	20024
X-RAY DIFFRACTION	f_dihedral_angle_d	17.055	5541
X-RAY DIFFRACTION	f_chiral_restr	0.089	2241
X-RAY DIFFRACTION	f_plane_restr	0.006	2500

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	505	X-RAY DIFFRACTION	POSITIONAL
1	2	B	505	X-RAY DIFFRACTION	POSITIONAL	0.08
2	1	A	419	X-RAY DIFFRACTION	POSITIONAL
2	2	B	419	X-RAY DIFFRACTION	POSITIONAL	0.079
3	1	A	1236	X-RAY DIFFRACTION	POSITIONAL
3	2	B	1236	X-RAY DIFFRACTION	POSITIONAL	0.058
4	1	A	402	X-RAY DIFFRACTION	POSITIONAL
4	2	B	402	X-RAY DIFFRACTION	POSITIONAL	0.045
5	1	A	909	X-RAY DIFFRACTION	POSITIONAL
5	2	B	909	X-RAY DIFFRACTION	POSITIONAL	0.042
6	1	A	2797	X-RAY DIFFRACTION	POSITIONAL
6	2	B	2797	X-RAY DIFFRACTION	POSITIONAL	0.05
7	1	A	178	X-RAY DIFFRACTION	POSITIONAL
7	2	B	178	X-RAY DIFFRACTION	POSITIONAL	0.038
8	1	E	179	X-RAY DIFFRACTION	POSITIONAL
8	2	F	179	X-RAY DIFFRACTION	POSITIONAL	0.035

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.187-3.3012	0.3237	202	0.2332	4196	X-RAY DIFFRACTION	97
3.3012-3.4333	0.2598	206	0.2018	4357	X-RAY DIFFRACTION	100
3.4333-3.5894	0.2418	203	0.1844	4351	X-RAY DIFFRACTION	100
3.5894-3.7785	0.248	206	0.1782	4391	X-RAY DIFFRACTION	100
3.7785-4.015	0.2313	185	0.163	4359	X-RAY DIFFRACTION	100
4.015-4.3246	0.1939	210	0.1294	4378	X-RAY DIFFRACTION	100
4.3246-4.7591	0.1381	187	0.115	4371	X-RAY DIFFRACTION	100
4.7591-5.446	0.1965	199	0.1422	4371	X-RAY DIFFRACTION	100
5.446-6.8549	0.2195	193	0.1865	4365	X-RAY DIFFRACTION	100
6.8549-38.1219	0.1997	203	0.2017	4302	X-RAY DIFFRACTION	99

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	0.7474	0.0869	-0.3122	1.022	-0.2878	0.8915	-0.0158	0.1545	-0.1436	-0.1019	-0.0301	-0.0944	0.2449	-0.0004	-0.0243	0.0648	0.0036	-0.0527	0.0822	-0.0629	0.0738	99.6553	21.4454	-20.2741
2	5.9203	-0.6256	0.3824	5.0301	-1.7887	1.1572	-0.1173	0.8305	0.1546	-0.222	-0.1453	-1.5157	0.1382	0.4411	0.0028	0.4464	0.1006	0.1423	0.3294	-0.0213	0.6883	117.2963	7.5789	-31.6441
3	2.1759	0.0303	-0.7636	0.9161	0.316	1.4554	0.2537	0.1576	0.2822	-0.4595	-0.1116	-0.6327	-0.1631	0.4892	-0.196	0.3337	0.1501	0.2329	0.4153	0.1156	0.4526	125.7622	39.5101	-43.6302
4	0.5504	0.0848	0.2205	0.5679	0.0579	0.7156	0.1189	-0.0074	-0.0966	0.1223	0.0615	-0.1969	0.0661	0.0734	-0.0145	0.0468	-0.0126	-0.0125	0.0155	0.0296	-0.0584	103.5866	34.1606	3.1871
5	1.2459	0.2871	-0.125	1.0554	-0.0385	1.0919	0.0135	0.0252	0.2277	-0.0566	0.0398	-0.2975	-0.2113	0.2759	0.0051	0.0632	-0.1364	-0.0453	0.1059	-0.0096	0.2416	121.2074	57.7277	0.6156
6	1.1996	-0.3196	-0.467	0.9503	-0.1659	1.5165	-0.1666	-0.1436	-0.1991	0.2211	0.0071	-0.1698	0.2273	0.2497	0.0142	0.1299	0.0237	-0.0383	0.0502	0.0185	0.128	190.1728	74.8197	22.6148
7	2.8976	-1.1365	-0.9878	2.3595	0.9519	2.4343	-0.2384	-0.1854	-0.7729	0.1898	-0.147	0.7323	0.2162	-0.3371	0.2305	0.2739	0.1506	0.2027	0.2543	0.0759	0.4545	195.4183	52.9732	33.6162
8	1.0113	0.2406	-0.2824	3.3092	-0.985	1.3759	-0.2101	-0.1099	-0.177	0.2539	0.3588	0.62	0.1406	-0.2926	-0.2402	0.5096	0.0741	0.2164	0.1841	0.1339	0.3115	162.6851	63.0293	41.7592
9	0.8763	-0.2433	0.2957	0.8763	-0.0837	0.7116	0.2027	0.247	-0.2825	-0.2693	-0.0637	-0.0253	0.2477	0.0515	-0.0189	0.1796	0.0939	-0.0043	0.0197	0.0147	0.0076	178.0417	76.2857	-1.7914
10	1.3567	0.0568	0.1258	0.7911	0.1108	0.8419	0.0182	-0.1089	-0.2177	-0.0589	-0.0014	0.2464	0.1742	-0.3571	-0.005	0.0971	-0.1261	-0.1636	0.241	0.0399	0.146	149.049	70.7535	-0.1257
11	0.052	0.0076	0.0148	0.0053	-0.0017	0.0172	0.0015	0.0133	-0.0198	-0.0004	0.0047	-0.0081	0.0037	0.006	-0.0239	0.0239	0.0045	-0.0223	0.0171	-0.0258	0.0423	107.9276	44.3556	-10.4682
12	0.0232	-0.0161	0.0242	0.0253	-0.0034	0.0388	0.0017	-0.0037	-0.012	-0.0339	-0.0021	0.0531	0.0049	-0.0277	-0.0853	0.0253	0.0448	-0.0533	0.0631	0.015	0.0841	166.5308	76.7295	11.6021

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 217:274 OR RESID 396:494 OR RESID 671:712 ) )	A	217 - 274
2	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 217:274 OR RESID 396:494 OR RESID 671:712 ) )	A	396 - 494
3	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 217:274 OR RESID 396:494 OR RESID 671:712 ) )	A	671 - 712
4	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 275:395 )	A	275 - 395
5	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 495:670 )	A	495 - 670
6	X-RAY DIFFRACTION	4	( CHAIN A AND ( RESID 722:773 OR RESID 947:1251 ) )	A	722 - 773
7	X-RAY DIFFRACTION	4	( CHAIN A AND ( RESID 722:773 OR RESID 947:1251 ) )	A	947 - 1251
8	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 774:946 )	A	774 - 946
9	X-RAY DIFFRACTION	6	( CHAIN B AND ( RESID 220:274 OR RESID 396:494 OR RESID 671:710 ) )	B	220 - 274
10	X-RAY DIFFRACTION	6	( CHAIN B AND ( RESID 220:274 OR RESID 396:494 OR RESID 671:710 ) )	B	396 - 494
11	X-RAY DIFFRACTION	6	( CHAIN B AND ( RESID 220:274 OR RESID 396:494 OR RESID 671:710 ) )	B	671 - 710
12	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 275:395 )	B	275 - 395
13	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 495:670 )	B	495 - 670
14	X-RAY DIFFRACTION	9	( CHAIN B AND ( RESID 722:773 OR RESID 947:1251 ) )	B	722 - 773
15	X-RAY DIFFRACTION	9	( CHAIN B AND ( RESID 722:773 OR RESID 947:1251 ) )	B	947 - 1251
16	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 774:946 )	B	774 - 946
17	X-RAY DIFFRACTION	11	( CHAIN E AND RESID 1:9 )	E	1 - 9
18	X-RAY DIFFRACTION	12	( CHAIN F AND RESID 1:9 )	F	1 - 9

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