PDB-2j7n: Structure of the RNAi polymerase from Neurospora crassa

ID or keywords:

Entry

Database: PDB / ID: 2j7n

Title

Structure of the RNAi polymerase from Neurospora crassa

Components

RNA-DEPENDENT RNA POLYMERASE

Keywords

HYDROLASE / RNAI RESPONSE / RNA-DIRECTED RNA POLYMERASE

Function / homology

Function and homology information

nuclear RNA-directed RNA polymerase complex / siRNA processing / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding / RNA binding / ATP binding / identical protein binding / metal ion binding
Similarity search - Function

Biological species

NEUROSPORA CRASSA (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Salgado, P.S. / Koivunen, M.R.L. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.

Citation

Journal: Plos Biol. / Year: 2006
Title: The Structure of an Rnai Polymerase Links RNA Silencing and Transcription.
Authors: Salgado, P.S. / Koivunen, M.R.L. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.

History

Deposition	Oct 13, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 13, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jul 5, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2j7n.cif.gz	407.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2j7n.ent.gz	322.4 KB	Display	PDB format
PDBx/mmJSON format	2j7n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2j7n_validation.pdf.gz	474.7 KB	Display	wwPDB validaton report
Full document	2j7n_full_validation.pdf.gz	578.1 KB	Display
Data in XML	2j7n_validation.xml.gz	85 KB	Display
Data in CIF	2j7n_validation.cif.gz	120.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7n ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7n	HTTPS FTP

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Related structure data

Related structure data	2j7oC C: citing same article (ref.)
Similar structure data	5fsw-2 5fsw-1 2j7o-1 3bga-d 7ns3-d 10817 3sq5-d 4k9w-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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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA-DEPENDENT RNA POLYMERASE

B: RNA-DEPENDENT RNA POLYMERASE

hetero molecules

234 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	101.021, 122.553, 114.701
Angle α, β, γ (deg.)	90.00, 108.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B
1	6	A
2	6	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	LYS	LYS	2	A	A	470 - 646	90 - 266
2	1	1	GLU	GLU	LYS	LYS	2	B	B	470 - 646	90 - 266
1	1	2	VAL	VAL	ARG	ARG	2	A	A	647 - 807	267 - 427
2	1	2	VAL	VAL	ARG	ARG	2	B	B	647 - 807	267 - 427
1	2	2	VAL	VAL	HIS	HIS	2	A	A	914 - 1161	534 - 781
2	2	2	VAL	VAL	HIS	HIS	2	B	B	914 - 1161	534 - 781
1	1	3	ARG	ARG	GLN	GLN	2	A	A	837 - 888	457 - 508
2	1	3	ARG	ARG	GLN	GLN	2	B	B	837 - 888	457 - 508
1	2	3	ALA	ALA	GLY	GLY	2	A	A	1196 - 1372	816 - 992
2	2	3	ALA	ALA	GLY	GLY	2	B	B	1196 - 1372	816 - 992
1	1	4	ASP	ASP	ASN	ASN	4	A	A	808 - 836	428 - 456
2	1	4	ASP	ASP	ASN	ASN	4	B	B	808 - 836	428 - 456
1	1	5	LYS	LYS	ARG	ARG	4	A	A	887 - 913	507 - 533
2	1	5	LYS	LYS	ARG	ARG	4	B	B	887 - 913	507 - 533
1	1	6	ILE	ILE	GLY	GLY	4	A	A	1162 - 1195	782 - 815
2	1	6	ILE	ILE	GLY	GLY	4	B	B	1162 - 1195	782 - 815

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	RNA-DEPENDENT RNA POLYMERASE / HYPOTHETICAL PROTEIN NCU07534.1 Mass: 116708.938 Da / Num. of mol.: 2 / Fragment: RESIDUES 381-1402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PEM69 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): INVSC1 / References: UniProt: Q9Y7G6
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 920 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 58.8 %
Crystal grow	Details: 100 MM TRISHCL PH 7.5, 150 MM NACL, 8% PEG 6000, AND 5 MM MGCL2.

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→20 Å / Num. obs: 114252 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 15.3 % / R_merge(I) obs: 0.1 / Net I/σ(I): 18.2
Reflection shell	Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SnB		phasing
SOLVE		phasing
REFMAC	5.2.0005	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.3→19.98 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.925 / SU B: 14.819 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A DIMER IS PRESENT IN THE ASYMMETRIC UNIT. HOWEVER EACH MONOMER HAS A NUMBER OF DOMAINS THAT ARE RELATED TO THEIR DIMERIC PARTNERS BY ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.264	5748	5 %	RANDOM
R_work	0.217	-	-	-
obs	0.219	108414	97.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 51.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	-0.09 Å²
2-	-	0.55 Å²	0 Å²
3-	-	-	-0.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15018	0	7	920	15945

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	15406
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.524	1.955	20850
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.063	5	1855
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.665	23.38	716
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.02	15	2684
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.136	15	116
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	2233
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11707
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.271	0.3	7930
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.328	0.5	10386
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.23	0.5	1487
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.251	0.3	72
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.393	0.5	23
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.568	1.5	9523
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.966	2	15057
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.34	3	6694
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.085	4.5	5793
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	584	tight positional	0.08	0.05
1	2	B	584	tight positional	0.08	0.05
2	1	A	1636	tight positional	0.09	0.05
2	2	B	1636	tight positional	0.09	0.05
3	1	A	828	tight positional	0.07	0.05
3	2	B	828	tight positional	0.07	0.05
1	1	A	572	medium positional	0.46	0.3
1	2	B	572	medium positional	0.46	0.3
2	1	A	1604	medium positional	0.43	0.3
2	2	B	1604	medium positional	0.43	0.3
3	1	A	871	medium positional	0.42	0.3
3	2	B	871	medium positional	0.42	0.3
4	1	A	241	medium positional	0.43	0.3
4	2	B	241	medium positional	0.43	0.3
5	1	A	233	medium positional	0.82	0.3
5	2	B	233	medium positional	0.82	0.3
6	1	A	268	medium positional	0.53	0.3
6	2	B	268	medium positional	0.53	0.3
1	1	A	584	tight thermal	0.9	5
1	2	B	584	tight thermal	0.9	5
2	1	A	1636	tight thermal	1.45	5
2	2	B	1636	tight thermal	1.45	5
3	1	A	828	tight thermal	0.88	5
3	2	B	828	tight thermal	0.88	5
1	1	A	572	medium thermal	1.15	7
1	2	B	572	medium thermal	1.15	7
2	1	A	1604	medium thermal	1.69	7
2	2	B	1604	medium thermal	1.69	7
3	1	A	871	medium thermal	1.19	7
3	2	B	871	medium thermal	1.19	7
4	1	A	241	medium thermal	1.52	7
4	2	B	241	medium thermal	1.52	7
5	1	A	233	medium thermal	1.42	7
5	2	B	233	medium thermal	1.42	7
6	1	A	268	medium thermal	0.87	7
6	2	B	268	medium thermal	0.87	7

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.355	455
R_work	0.305	7801

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	3.0509	0.9932	0.0525	5.3654	-0.1862	2.3665	0.0756	0.2729	0.9239	-0.0414	0.0879	0.8921	-0.5755	-0.4857	-0.1635	0.1034	0.1602	0.0091	-0.1085	0.149	0.2566	46.963	85.1208	47.7432
2	1.4366	-0.0001	-0.5943	0.4898	0.0632	1.4531	0.073	0.0434	-0.0048	-0.0944	-0.0595	0.0725	0.1103	-0.1785	-0.0136	-0.1791	0.0107	-0.0231	-0.2834	-0.0104	-0.1722	51.8377	56.7643	67.2763
3	3.1055	-0.4905	-0.5983	3.165	-0.9605	5.7841	0.0271	0.2201	0.1417	0.2302	0.0987	0.3586	-0.6385	-1.4584	-0.1258	-0.1104	0.1542	0.064	0.0976	0.0027	-0.2006	61.4774	104.1847	82.6035
4	8.2318	14.0399	0.4114	24.2465	0.9692	0.686	0.24	0.061	-0.0032	0.2116	-0.0113	-0.2319	-0.3176	0.154	-0.2287	-0.0276	-0.0627	0.0708	-0.0595	-0.0334	-0.1394	51.7376	71.2588	96.9307
5	4.0921	11.963	0.3127	34.9734	0.9142	0.0239	-0.0643	0.1316	0.6172	-0.2992	-0.0361	1.8304	-0.17	0.1696	0.1004	0.1188	-0.0213	0.0031	0.1983	-0.017	0.0842	49.6862	83.6822	88.7772
6	10.0745	10.2257	6.7615	21.1375	10.9708	11.77	-0.3015	-0.7618	1.1448	0.0251	-0.3108	0.1323	-1.5732	0.2373	0.6122	0.1007	-0.0968	0.0073	0.0948	-0.0591	0.1419	45.8145	83.1803	98.9139
7	4.9493	1.277	0.288	7.3166	0.0709	3.7509	0.0587	-0.3024	1.4241	0.0668	0.0577	-0.3456	-1.5877	0.7228	-0.1164	0.6045	-0.3662	0.1467	0.3365	-0.3646	0.448	100.1724	85.1662	119.8034
8	2.4255	0.2835	-0.7183	0.5677	-0.1223	2.2886	0.1706	-0.319	0.1217	0.062	-0.0362	-0.0701	-0.012	0.2445	-0.1344	-0.2055	-0.0309	-0.0267	-0.2741	-0.0164	-0.1599	96.8062	57.3107	98.7019
9	2.1954	0.5102	-0.3697	2.7835	-0.977	5.4472	-0.0103	0.0309	0.1715	0.1998	-0.1377	-0.3693	-0.6445	0.4527	0.1481	-0.0898	-0.0456	0.0051	-0.2526	0.0231	-0.1362	82.965	106.2471	77.9687
10	14.6637	-21.0211	2.146	30.1408	-3.0427	0.5007	0.6165	-0.1507	0.3233	-1.0158	-0.0692	-0.0462	0.0398	-0.2486	-0.5473	0.0626	0.0625	0.1234	-0.1221	0.0215	0.037	96.4786	71.9781	67.3835
11	10.0526	-14.2941	0.9936	21.2878	-1.6947	0.1807	0.0695	0.2209	0.3474	0.0741	-0.459	-1.253	0.0403	0.3353	0.3895	0.0871	0.0928	-0.042	0.0716	0.0008	0.1319	97.3901	87.1108	73.6408
12	8.8983	-12.663	8.1288	36.2595	-20.7792	17.1842	0.015	0.8874	0.9819	-0.5206	-0.1321	0.2734	-1.2232	-0.2096	0.1171	0.1649	0.0749	0.036	0.0999	0.0542	0.2518	102.3328	84.2474	64.8229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	390 - 646
2	X-RAY DIFFRACTION	2	A	647 - 807
3	X-RAY DIFFRACTION	2	A	914 - 1161
4	X-RAY DIFFRACTION	3	A	837 - 888
5	X-RAY DIFFRACTION	3	A	1196 - 1372
6	X-RAY DIFFRACTION	4	A	808 - 836
7	X-RAY DIFFRACTION	5	A	889 - 913
8	X-RAY DIFFRACTION	6	A	1162 - 1195
9	X-RAY DIFFRACTION	7	B	390 - 646
10	X-RAY DIFFRACTION	8	B	647 - 807
11	X-RAY DIFFRACTION	8	B	914 - 1161
12	X-RAY DIFFRACTION	9	B	837 - 888
13	X-RAY DIFFRACTION	9	B	1196 - 1372
14	X-RAY DIFFRACTION	10	B	808 - 836
15	X-RAY DIFFRACTION	11	B	889 - 913
16	X-RAY DIFFRACTION	12	B	1162 - 1195

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi