PDB-3kio: mouse RNase H2 complex

ID or keywords:

Entry

Database: PDB / ID: 3kio

Title

mouse RNase H2 complex

Components

Ribonuclease H2 subunit A
Ribonuclease H2 subunit B
Ribonuclease H2 subunit C

Keywords

HYDROLASE /

ribonuclease / Aicardi-Goutieres syndrome / RNase H2 /

protein complex / autoimmune disease /

Endonuclease / Metal-binding /

Nuclease /

Nucleus /

Phosphoprotein /

Acetylation

Function / homology

Function and homology information

ribonucleotide metabolic process / ribonuclease H2 complex /

DNA replication, removal of RNA primer /

regulation of DNA damage checkpoint / RNA catabolic process /

ribonuclease H /

mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.9 Å

Authors

Shaban, N. / Harvey, S. / Perrino, F.W. / Hollis, T.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: The structure of the mammalian RNase H2 complex provides insight into RNA:DNA hybrid processing to prevent immune dysfunction.
Authors: Shaban, N.M. / Harvey, S. / Perrino, F.W. / Hollis, T.

History

Deposition	Nov 2, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kio.cif.gz	214.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3kio.ent.gz	172.8 KB	Display	PDB format
PDBx/mmJSON format	3kio.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/ki/3kio ftp://data.pdbj.org/pub/pdb/validation_reports/ki/3kio	HTTPS FTP

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Related structure data

Similar structure data	5z24-1 1j09-d 1n75-d 3dy6-2 2l5x-d 3fbt-2 3aii-d 4dy7-2 3fbt-1 5hpf-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
Related items in Molecule of the Month	#135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: Ribonuclease H2 subunit A

B: Ribonuclease H2 subunit B

C: Ribonuclease H2 subunit C

89.5 kDa, 3 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)	279.287, 40.421, 67.820
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Ribonuclease H2 subunit A / RNase H2 subunit A / Ribonuclease HI subunit A / Ribonuclease HI large subunit / RNase HI large subunit Mass: 33782.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: RNase H2A, Rnaseh2a, Rnasehi / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CWY8, ribonuclease H
#2: Protein	Ribonuclease H2 subunit B / RNase H2 subunit B / Ribonuclease HI subunit B / Deleted in lymphocytic leukemia 8 homolog Mass: 37771.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dleu8, RNase H2B, Rnaseh2b / Plasmid: pCDFduet / Production host: Escherichia coli (E. coli) / References: UniProt: Q80ZV0
#3: Protein	Ribonuclease H2 subunit C / RNase H2 subunit C / Ribonuclease HI subunit C Mass: 17955.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ayp1, RNase H2C, Rnaseh2c / Plasmid: pCDFduet / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQ18
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.14 Å³/Da / Density % sol: 42.48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.9798, 0.979, 0.9795

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9798	1
2	0.979	1
3	0.9795	1

Reflection

Resolution: 2.6→30 Å / Num. all: 24694 / Num. obs: 23731 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / R_merge(I) obs: 0.113 / Net I/σ(I): 12.1

Reflection shell

Resolution: 2.6→2.69 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1805

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.4_113)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.9→24.619 Å / SU ML: 0.47 / σ(F): 1.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3055	1692	5.2 %	random 5%
R_work	0.2339	-	-	-
obs	0.2381	22814	99.27 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.771 Å² / k_sol: 0.281 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.9→24.619 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3794	0	0	60	3854

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3877
X-RAY DIFFRACTION	f_angle_d	1.352	5275
X-RAY DIFFRACTION	f_dihedral_angle_d	21.759	1352
X-RAY DIFFRACTION	f_chiral_restr	0.085	603
X-RAY DIFFRACTION	f_plane_restr	0.007	693

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 (%)
2.9-3.0035	0.3125	190	0.251	3041	X-RAY DIFFRACTION	100
3.0035-3.1235	0.3126	176	0.2177	3105	X-RAY DIFFRACTION	100
3.1235-3.2654	0.302	146	0.2151	3092	X-RAY DIFFRACTION	100
3.2654-3.4371	0.324	150	0.2126	3144	X-RAY DIFFRACTION	99
3.4371-3.6518	0.2907	171	0.2119	3075	X-RAY DIFFRACTION	99
3.6518-3.9327	0.3076	174	0.2285	3093	X-RAY DIFFRACTION	99
3.9327-4.3265	0.2943	181	0.2127	3032	X-RAY DIFFRACTION	99
4.3265-4.9482	0.303	167	0.1986	3090	X-RAY DIFFRACTION	98
4.9482-6.2175	0.3321	173	0.2426	3089	X-RAY DIFFRACTION	100
6.2175-24.6195	0.2624	164	0.2704	3113	X-RAY DIFFRACTION	100

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	0.149	0.1985	0.0608	0.3461	0.0326	0.1014	-2.1638	-1.5602	-0.9935	0.4454	-1.7393	0.0141	0.4219	-1.83	-0.0273	1.6721	-0.4955	-0.4067	1.5083	0.1466	0.8612	29.0703	0.2527	9.4353
2		0.8644	-0.1501	-1.0905	3.1311	0.8101	1.4111	0.4411	-0.2155	0.0249	-0.903	-0.1378	-0.6674	-0.1016	0.3983	0.0394	0.1913	0.0673	-0.0348	0.1672	0.0418	0.2487
3		0.9587	0.0121	0.5195	0.661	-0.2274	0.0323	0.3585	-0.8379	0.1505	-0.511	-0.1222	-0.459	0.1803	-0.386	0.0221	0.293	-0.0391	0.0397	0.1978	-0.0724	0.1494
4		0.5557	-0.1481	0.4137	0.069	-0.2402	0.4993	0.4472	0.2654	1.0166	0.4573	-1.0433	-1.5125	-0.6053	0.8469	-0.0025	1.0847	-0.0806	0.0815	1.0665	-0.03	0.6882
5		2.1352	-0.3147	1.3539	2.1243	0.3209	0.7307	0.3299	1.4626	-1.4682	-0.3965	0.035	0.2755	0.2295	0.9623	0.0553	0.104	0.1414	0.0156	0.5487	0.0061	0.218
6		3.2255	1.0019	2.8757	1.1729	1.2464	2.8027	0.1124	-1.6608	-0.059	-0.0056	-0.4352	0.5932	-0.7458	-0.7637	-0.1105	0.3366	-0.1417	-0.0987	0.4683	-0.0013	0.0529
7		1.8236	-0.8113	0.9595	3.359	0.0701	0.5132	-0.2069	-0.7779	-0.2384	1.1854	0.3191	-0.1003	0.0372	-0.7285	0.0188	0.0924	-0.0238	0.05	0.1826	0.0494	0.0451
8		1.3654	0.4316	-0.482	1.5707	-0.438	2.2733	-0.0882	-0.33	0.2177	0.5243	0.0226	-0.2085	0.0228	0.0543	-0.0006	0.1922	0.0042	-0.0376	0.2498	-0.0654	0.1812
9		1.781	0.0172	0.385	1.8321	-0.3212	2.2812	-0.1616	-0.5285	1.3383	0.0819	0.7755	0.7857	-0.3264	-0.4342	0.1097	0.1306	-0.0607	-0.0653	0.1593	0.0216	0.1981
10		1.1236	0.7845	-0.1855	1.9374	0.7717	3.3471	0.0585	0.1845	-0.8035	-0.1019	-0.3496	-1.0202	-0.5124	-0.303	-0.0165	0.2183	-0.104	0.0475	0.1778	0.0006	0.3582
11		1.2728	-0.1714	-0.6265	1.3611	0.7907	0.9506	0.3868	0.1663	0.5795	0.1078	-0.5677	-1.2185	0.7721	-0.2002	0.0421	0.4342	0.0293	-0.0541	0.1758	0.0398	0.0138
12		4.5059	0.7053	3.0928	3.7642	1.5974	8.3098	0.036	0.9207	0.0263	0.2096	0.6396	0.0486	-1.6631	1.0447	0.6238	0.0944	0.152	-0.0005	-0.0985	0.0406	0.2055
13		4.3882	-2.0092	-1.6352	3.4886	0.5343	3.9644	-0.2799	1.2247	0.0837	-0.0914	-0.6258	0.4083	0.2233	-0.3199	-1.7524	0.1042	-0.1358	0.0372	0.2416	-0.0052	0.1493
14		0.4816	1.5719	-1.0808	6.4505	-2.3727	3.2786	-0.0262	0.09	0.7779	1.2332	0.5077	1.7914	-0.2083	-1.5547	0.2022	0.458	0.0807	0.1166	0.3273	-0.0328	0.2084
15		0.3557	-0.8292	-0.9629	2.3621	2.8683	3.5525	0.6887	0.2513	0.9941	-0.841	-1.3434	-0.1738	-1.6685	-0.7888	0.3978	0.1772	-0.1725	-0.5252	0.2609	-0.0048	0.4726
16		0.2937	-0.171	0.0663	0.2296	-0.2082	0.3453	-0.3014	-1.1843	-1.0253	-1.0861	-0.3107	-1.28	0.6036	-0.6347	-0.0251	0.4686	-0.1249	-0.1767	0.4151	-0.2614	1.7952
17		0.4398	-0.3074	0.3848	1.1069	-0.6496	0.4803	-1.628	1.133	1.2284	0.9524	0.6668	0.584	-0.9341	-1.9644	0.0041	1.1173	0.3569	-0.6787	1.3073	-0.511	1.8225
18		1.5527	-0.0934	-0.3984	9.2953	-5.549	3.5735	-0.5207	-2.0652	0.3072	1.7501	0.7513	0.8185	-0.7119	-1.548	-0.2015	0.4768	-0.1574	-0.214	1.9124	0.4283	2.0418
19		0.2951	0.3936	-0.1081	0.5517	-0.0689	0.293	0.2048	-0.6225	-2.3305	-1.0009	0.4484	2.1031	-0.6189	-0.4034	-0.0012	0.3657	-0.1154	-0.5238	0.6326	-0.3125	2.1168
20		0.4142	0.0987	-0.4648	0.2302	-0.1052	0.4689	-0.2175	-0.3293	1.3246	-0.4656	-0.2872	1.4299	-0.6233	0.0247	-0.0011	0.2083	-0.0178	-0.0661	0.5712	0.0841	1.0917
21		0.6763	0.4544	-0.5942	0.8404	-1.1162	1.7874	0.1786	-0.1907	0.837	-0.4474	0.8421	-0.0831	0.4609	-0.7042	0.0256	0.1641	-0.0807	0.0227	0.2726	-0.0402	0.2859
22		0.5536	0.2179	-0.4946	0.4477	-0.4541	0.5688	-0.579	0.42	0.2462	-0.5746	0.0725	1.1183	0.194	0.4082	-0.0244	0.1063	-0.0785	-0.022	0.473	-0.1274	0.4782
23		0.0082	0.1004	0.0553	0.3551	-0.1309	0.0634	-0.8497	1.178	0.0083	-0.8901	-0.1934	2.5673	0.5657	-0.4909	-0.0035	0.5284	-0.0733	-0.1126	0.4102	-0.1183	1.08
24		0.1895	-0.0309	-0.0322	1.2379	-0.9496	0.7218	-1.6771	-1.2552	-0.7935	1.8816	-0.0355	0.7656	1.3926	0.5784	-0.0347	0.3708	0.0527	0.3898	0.5975	-0.2418	0.8261
25		0.1449	-0.2153	0.0644	0.2269	-0.1439	0.0005	0.4682	0.2538	0.1324	0.7714	0.4376	2.3336	0.1477	0.7125	0.0002	1.2101	-0.4361	0.0127	1.0415	0.1484	1.6748
26		0.1096	-0.0735	-0.1768	0.1731	0.0547	0.3072	-0.4163	-0.5144	-0.3481	0.9866	-0.3697	1.8944	1.1426	-0.8622	0.0014	0.5816	-0.0345	0.1742	1.0206	0.0032	2.0106
27		0.4218	0.1279	-0.0669	0.02	-0.0511	0.7625	-0.9495	-0.2359	-1.6201	1.1152	-0.5029	0.3011	0.1174	0.7657	-0.0044	0.8318	-0.1517	-0.0848	0.6192	0.1273	1.1535
28		0.1264	-0.1449	0.0837	0.117	-0.0702	0.05	-1.3712	3.2231	0.259	-0.1455	-0.5976	-0.5682	-0.6733	0.3646	0.003	1.3731	-0.5943	-0.4562	0.7054	0.0127	0.6356
29		0.6192	0.7129	0.451	0.907	0.6787	1.4831	0.5574	0.6301	-1.918	-1.3189	0.9639	-1.1658	0.54	-0.1147	0.0281	0.6468	-0.3093	-0.0355	0.5636	-0.1292	0.6006
30		1.4388	1.9767	1.2876	2.6912	2.0996	6.2156	-0.4629	0.4035	1.0189	-0.2916	-0.2461	1.6973	-1.8532	-1.1598	-0.769	-0.078	-0.0944	0.3237	0.1969	0.1324	0.0585
31		8.1934	-0.4702	4.3027	6.0185	-0.9647	5.0302	1.4241	2.5621	0.2955	-1.4543	-0.3511	-0.3461	0.9027	1.9751	0.3662	0.4097	0.1907	0.1429	0.5547	0.0355	0.1488
32		4.2547	-2.8703	1.3468	4.829	-4.375	7.7198	-0.2767	1.0057	1.2223	0.2487	-0.2922	-0.4508	1.0157	0.7437	-0.1921	0.1791	-0.0677	-0.0523	0.1263	-0.0054	0.168
33		4.6626	3.2605	4.6072	3.1035	3.6337	4.7516	0.8754	-0.0287	-1.2729	0.5467	0.1438	-1.0783	1.1654	0.2389	0.3378	0.1702	0.3139	0.0783	0.1575	0.0248	0.5358
34		1.3506	-1.0891	-1.5549	4.8841	4.8565	5.1167	-0.0775	-0.8666	-0.1814	1.3777	1.0489	0.2037	1.2585	1.4693	0.1642	0.0251	-0.1458	-0.2253	0.2031	-0.029	0.3377
35		0.7739	0.1397	-1.1385	4.8732	3.5524	4.4257	0.076	-1.2544	-0.4081	0.8975	-0.1936	-0.4671	1.0711	0.6042	0.0392	0.1097	0.007	-0.0453	0.2518	-0.0062	0.3717
36		0.9138	0.3809	-0.9033	0.4811	-0.5492	1.0092	1.3351	-0.9205	-0.7294	0.2009	-0.2757	-0.0005	1.5271	0.3007	-0.0138	0.4609	-0.0084	-0.2011	0.3286	0.111	0.8528
37		1.8263	-0.5905	-3.2658	0.6386	1.2173	6.4498	-0.3711	0.9119	0.3544	-1.0862	0.402	2.8841	1.7537	-0.1136	-0.181	0.3886	-0.1227	-0.3652	0.5528	-0.1432	0.7784
38		0.0878	0.0206	-0.0743	0.005	-0.0212	0.0656	-1.4056	-0.1747	-0.3139	-1.4646	1.0335	0.9603	0.6348	0.709	0.0165	0.7549	-0.2397	0.0538	1.0188	-0.0393	0.9071
39		0.8937	-0.2341	-0.1355	0.2352	0.006	0.0779	0.1807	-0.9182	0.7058	-0.0443	-0.733	-0.8239	-0.336	-0.5296	-0.0087	0.236	-0.0396	-0.1401	0.229	-0.0795	0.4714
40		1.0241	-0.0691	-0.7438	7.3448	8.0096	2.0403	0.9043	0.0725	0.1733	0.3549	-1.0269	-0.1194	-0.7833	-1.4053	-0.3293	0.3603	0.0886	-0.0342	0.1551	0.0047	0.1689
41		0.3281	-0.0481	-0.0944	0.4273	0.299	0.1955	-0.5162	-0.8453	0.3109	-1.1346	-1.1456	1.101	2.0509	-1.5934	0.0112	1.3772	-0.5408	-0.194	0.5923	0.1346	0.9511
42		0.2791	-0.2884	0.1509	0.397	-0.2504	0.1676	1.2414	-0.7001	1.1864	1.7536	-2.9591	-1.3224	-0.8542	0.5534	-0.032	0.5977	-0.1583	0.1013	0.6091	-0.0322	0.7661
43		0.1874	-0.0722	0.3953	0.034	-0.1348	0.5968	0.5674	-2.0374	2.8686	2.0793	-0.4722	0.9646	1.7555	-0.8746	-0.0104	2.0802	-0.1381	-0.1543	0.743	-0.064	1.0796

Refinement TLS group

Selection details: chain C and resid 136:144)

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About Yorodumi

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Yorodumi