PDB-9m0h: Crystal structure of human endonuclease G mutant C113A/H141A

ID or keywords:

Entry

Database: PDB / ID: 9m0h

Title

Crystal structure of human endonuclease G mutant C113A/H141A

Components

Endonuclease G, mitochondrial

Keywords

APOPTOSIS / His-Me finger endonucleases

Function / homology

Function and homology information

mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of mitochondrial DNA replication / positive regulation of apoptotic DNA fragmentation / single-stranded DNA endonuclease activity / apoptotic DNA fragmentation / negative regulation of TOR signaling / response to mechanical stimulus / RNA endonuclease activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Yang, W.Z. / Yuan, H.S.

Funding support

Taiwan, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Resveratrol isomers with opposing activities target endonuclease G to modulate neurodegeneration and mitochondrial elimination.
Authors: Lin, J.L.J. / Wu, X. / Redweik, G.A.J. / Chiu, C.C. / Chiu, T.J. / Chen, Y.P. / Webb, K.J. / Rani, R. / Lee, E.S. / Yang, W.Z. / Bhadra, J. / Stowell, M.H.B. / Yuan, H.S. / Xue, D.

History

Deposition	Feb 24, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 10, 2026	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9m0h.cif.gz	270.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9m0h.ent.gz	220.2 KB	Display	PDB format
PDBx/mmJSON format	9m0h.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/m0/9m0h ftp://data.pdbj.org/pub/pdb/validation_reports/m0/9m0h	HTTPS FTP

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Related structure data

Related structure data	9m0gC 9m1eC 6njtS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: Endonuclease G, mitochondrial

B: Endonuclease G, mitochondrial

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.992, 73.745, 89.539
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Endonuclease G, mitochondrial / Endo G Mass: 33695.270 Da / Num. of mol.: 2 / Mutation: C113A,H141A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENDOG / Production host: Escherichia coli (E. coli) References: UniProt: Q14249, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.67 Å³/Da / Density % sol: 26.15 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane pH 8.0, 16% w/v Polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: TPS 05A / Wavelength: 0.99984 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 4, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.99984 Å / Relative weight: 1

Reflection

Resolution: 1.85→30 Å / Num. obs: 39047 / % possible obs: 99.6 % / Redundancy: 7 % / R_merge(I) obs: 0.053 / Χ²: 0.037 / Net I/σ(I): 15.7 / Num. measured all: 272549

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
1.85-1.88	6.8	0.574	1920	0.791	1	100
1.88-1.92	7	0.479	1919	0.809	1	100
1.92-1.95	7.1	0.408	1946	0.833	1	100
1.95-1.99	7.2	0.324	1919	0.876	1	100
1.99-2.04	7.3	0.28	1955	0.908	1	100
2.04-2.08	7.3	0.237	1917	0.944	1	99.9
2.08-2.14	7.3	0.194	1954	0.938	1	100
2.14-2.19	7.3	0.157	1912	0.911	1	100
2.19-2.26	7.3	0.129	1948	0.909	1	100
2.26-2.33	7.3	0.103	1934	0.868	1	100
2.33-2.41	7.3	0.084	1950	0.846	1	100
2.41-2.51	7.3	0.069	1953	0.793	1	100
2.51-2.62	7.2	0.054	1949	0.804	1	100
2.62-2.76	7.2	0.049	1955	0.875	1	100
2.76-2.94	7	0.04	1955	0.961	1	99.9
2.94-3.16	6.8	0.031	1962	0.901	1	99.9
3.16-3.48	6.6	0.024	1991	0.814	1	99.9
3.48-3.98	6.4	0.021	2000	0.796	1	100
3.98-5.01	6.2	0.02	2003	0.758	1	99.1
5.01-30	5.7	0.02	2005	0.72	1	93.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
DENZO		data reduction
SCALEPACK		data scaling
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NJT

6njt

Resolution: 1.85→25.63 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2053	1994	5.12 %
R_work	0.1723	-	-
obs	0.174	38983	99.29 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→25.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3424	0	2	464	3890

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	6.302	484
X-RAY DIFFRACTION	f_chiral_restr	0.065	509
X-RAY DIFFRACTION	f_plane_restr	0.014	628

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 (%)
1.85-1.89	0.2818	121	0.2111	2532	X-RAY DIFFRACTION	96
1.89-1.94	0.2152	145	0.1944	2588	X-RAY DIFFRACTION	100
1.94-2	0.2041	147	0.1746	2625	X-RAY DIFFRACTION	100
2-2.07	0.217	140	0.1709	2616	X-RAY DIFFRACTION	100
2.07-2.14	0.216	139	0.1675	2625	X-RAY DIFFRACTION	100
2.14-2.23	0.1949	142	0.1667	2641	X-RAY DIFFRACTION	100
2.23-2.33	0.2035	136	0.1581	2654	X-RAY DIFFRACTION	100
2.33-2.45	0.199	153	0.168	2636	X-RAY DIFFRACTION	100
2.45-2.6	0.194	141	0.1685	2629	X-RAY DIFFRACTION	100
2.6-2.8	0.2385	134	0.1753	2687	X-RAY DIFFRACTION	100
2.8-3.09	0.2324	155	0.1848	2658	X-RAY DIFFRACTION	100
3.09-3.53	0.1985	148	0.1643	2678	X-RAY DIFFRACTION	100
3.53-4.44	0.1737	144	0.1521	2713	X-RAY DIFFRACTION	100
4.45-25.63	0.2053	149	0.1921	2707	X-RAY DIFFRACTION	95

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	5.6078	2.5404	1.062	8.6628	1.5661	3.5948	-0.0855	0.1777	-0.3919	-0.532	0.1729	-0.2505	0.4745	-0.1092	-0.0494	0.2003	-0.0597	-0.0123	0.1298	-0.0001	0.1089	-4.9098	-13.526	4.5996
2	2.4763	0.9516	0.4487	1.3974	1.0822	2.658	-0.0314	-0.1219	-0.3108	0.1864	0.0787	-0.1493	0.3992	0.1791	-0.0774	0.199	0.0243	-0.0146	0.1083	0.038	0.1462	10.6164	-4.3151	18.9823
3	2.8973	1.3383	0.8304	3.772	1.1169	3.9688	-0.0116	0.2701	-0.2005	-0.1727	0.1788	-0.2901	0.0609	0.3762	-0.0229	0.1271	0.041	0.0401	0.1756	0.0153	0.1735	19.9925	-0.053	8.3
4	2.1615	-0.0702	0.6884	3.0251	-0.1993	3.6701	-0.2309	-0.7078	-0.5367	0.6128	0.2788	-0.2354	0.5171	0.3581	-0.0835	0.2888	0.1312	-0.0022	0.3089	0.1311	0.2292	21.1923	-4.3392	26.0355
5	0.9671	0.7016	-0.248	3.1658	1.8196	4.7307	-0.0268	-0.1682	-0.0591	0.1431	0.1475	-0.3043	-0.0272	0.8084	-0.1114	0.0846	0.0245	-0.0247	0.2238	0.0364	0.1395	22.5749	9.0825	22.8737
6	1.8197	0.4757	1.0194	0.7395	0.5615	3.3355	-0.2202	0.0694	0.2203	0.014	0.0999	0.0944	-0.2567	0.0138	0.124	0.1625	0.0065	-0.0495	0.0189	0.0263	0.1417	10.7244	12.0358	16.8049
7	1.1146	-0.2524	-2.2237	0.9944	0.7193	8.6235	-0.0757	-0.3439	0.0816	0.0672	0.1186	-0.1602	-0.3603	0.7738	-0.1285	0.2085	-0.007	-0.0701	0.1597	-0.0014	0.182	17.2115	17.3005	26.8106
8	9.0172	2.5333	0.8217	6.6613	1.9486	3.5218	0.0033	-0.5817	0.311	0.2196	-0.3677	0.458	-0.3164	-0.3114	0.3047	0.1914	0.0404	-0.0626	0.1658	-0.0403	0.1282	6.3496	16.374	26.1461
9	2.5817	0.3144	3.1466	3.2273	1.301	4.3886	0.3464	-1.3717	-0.1874	0.814	-0.2999	-0.2711	0.1081	-0.2653	-0.0403	0.2504	-0.0404	-0.0515	0.3813	-0.0337	0.177	-6.9093	4.4503	19.6293
10	5.8772	-1.1122	0.2736	1.9706	0.1653	1.5603	-0.1752	-0.3391	0.4344	-0.2795	0.0657	0.7624	-0.146	-0.6216	0.0527	0.1963	0.0118	-0.0276	0.2679	-0.0292	0.3184	-21.3398	4.102	7.9312
11	1.6613	-0.63	1.0325	2.6716	0.2865	3.3109	-0.3067	-0.4763	0.5104	-0.0102	-0.0775	0.2417	-0.3637	-0.6436	0.2659	0.1765	0.0939	-0.087	0.2415	-0.1165	0.2918	-11.7097	16.999	13.3622
12	5.8456	1.2031	-0.4684	5.3023	0.6902	4.4855	-0.2251	-0.4194	0.1338	0.0989	0.0496	0.992	-0.0723	-0.7127	0.0194	0.0997	0.0432	-0.0207	0.3065	-0.0231	0.3228	-24.2062	5.3018	9.1541
13	2.7844	1.2309	0.7238	5.2329	0.6252	2.9036	-0.1408	0.1842	0.2886	-0.7022	0.1474	0.4115	-0.1753	-0.327	0.0294	0.1525	0.0164	-0.0847	0.1806	0.0194	0.1561	-16.958	6.2611	-2.5138
14	5.383	0.1905	-0.5542	1.0361	0.429	2.2786	0.333	-0.4373	0.1015	-0.1928	-0.2834	0.0387	0.0448	0.138	-0.0569	0.1909	0.0324	-0.0349	0.0617	0.0249	0.0573	-4.0906	1.1457	-0.6607
15	7.5218	-6.105	-5.887	6.8684	2.4895	7.5675	-0.0256	-0.2592	0.5388	-0.5222	0.1068	0.0304	-0.4083	0.2906	-0.2357	0.1058	-0.0324	-0.0878	0.1023	-0.0343	0.1599	2.6212	16.0739	4.805
16	2.1997	0.2706	0.4585	3.2742	-0.6852	2.0803	-0.1405	0.3012	0.0169	-0.6371	0.1595	0.1531	0.2065	-0.1048	-0.0125	0.1743	-0.0093	-0.008	0.1347	0.0028	0.0683	-9.8858	0.923	-2.5465
17	8.2122	-1.3953	5.6428	4.1372	-1.3193	8.1906	0.3005	0.4749	-0.2579	-0.7049	-0.2779	-0.1556	0.7365	0.1639	-0.0446	0.288	-0.0277	0.0529	0.1474	-0.0189	0.0799	-3.2251	-3.3117	-4.6384

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 275 through 288 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 through 125 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 126 through 141 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 142 through 160 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 161 through 188 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 237 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 238 through 259 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 260 through 283 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 65 through 90 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 91 through 115 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 116 through 141 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 142 through 160 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 161 through 188 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 189 through 210 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 211 through 220 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 221 through 259 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 260 through 274 )

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