PDB-7ndh: Crystal structure of ZC3H12C PIN domain

ID or keywords:

Entry

Database: PDB / ID: 7ndh

Title

Crystal structure of ZC3H12C PIN domain

Components

Probable ribonuclease ZC3H12C

Keywords

RNA BINDING PROTEIN / Endo-ribonuclease / regnase

Function / homology

Function and homology information

RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / Hydrolases; Acting on ester bonds / mRNA binding / nucleus / metal ion binding
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

Garg, A. / Heinemann, U.

Citation

Journal: Nucleic Acids Res. / Year: 2021
Title: PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.
Authors: Garg, A. / Roske, Y. / Yamada, S. / Uehata, T. / Takeuchi, O. / Heinemann, U.

History

Deposition	Feb 1, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 19, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 2, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ndh.cif.gz	159.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ndh_validation.pdf.gz	440.2 KB	Display	wwPDB validaton report
Full document	7ndh_full_validation.pdf.gz	441.6 KB	Display
Data in XML	7ndh_validation.xml.gz	17.1 KB	Display
Data in CIF	7ndh_validation.cif.gz	24.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nd/7ndh ftp://data.pdbj.org/pub/pdb/validation_reports/nd/7ndh	HTTPS FTP

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Related structure data

Related structure data	7ndiC 7ndjC 7ndkC 3v34S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ndh-2 2jar-d 4o7k-d 5fgp-d 1q92-d 1z4k-d 3goy-2 5x07-1 2kcu-d 4wvz-1 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	#245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: Probable ribonuclease ZC3H12C

B: Probable ribonuclease ZC3H12C

hetero molecules

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

1

A: Probable ribonuclease ZC3H12C

hetero molecules

defined by author
Evidence: gel filtration
20 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Probable ribonuclease ZC3H12C

hetero molecules

defined by author
20 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.331, 80.331, 143.202
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ASP	ASP	VAL	VAL	chain A	A	A	260 - 428	1 - 169
2	GLY	GLY	PRO	PRO	chain B	B	B	262 - 426	3 - 167

#1: Protein	Probable ribonuclease ZC3H12C / Zinc finger CCCH domain-containing protein 12C Mass: 19706.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12c, Kiaa1726 / Production host: Escherichia coli (E. coli) References: UniProt: Q5DTV4, Hydrolases; Acting on ester bonds
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.93 Å³/Da / Density % sol: 58.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 20% PEG 6000 and 0.1 M HEPES pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.94→44.5 Å / Num. obs: 35462 / % possible obs: 99.88 % / Redundancy: 7.53 % / CC_1/2: 0.999 / Net I/σ(I): 20.5
Reflection shell	Resolution: 1.94→2.06 Å / Num. unique obs: 3484 / CC_1/2: 0.692 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data scaling
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3v34

3v34

Resolution: 1.94→44.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2133	1774	5 %
R_work	0.1723	33688	-
obs	0.1744	35462	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 122.35 Å² / B_iso mean: 42.8204 Å² / B_iso min: 19.24 Å²

Refinement step

Cycle: final / Resolution: 1.94→44.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2712	0	33	260	3005
B_iso mean	-	-	45.63	48.99	-
Num. residues	-	-	-	-	334

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	2803
X-RAY DIFFRACTION	f_angle_d	1.399	3769
X-RAY DIFFRACTION	f_chiral_restr	0.074	401
X-RAY DIFFRACTION	f_plane_restr	0.008	493
X-RAY DIFFRACTION	f_dihedral_angle_d	11.777	1073

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1568	X-RAY DIFFRACTION	7.207	TORSIONAL
1	2	B	1568	X-RAY DIFFRACTION	7.207	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.94-1.9922	0.2932	134	0.2626	2534	99
1.9922-2.0508	0.2443	134	0.235	2551	100
2.0508-2.117	0.2789	133	0.2144	2522	100
2.117-2.1926	0.2416	134	0.1906	2554	100
2.1926-2.2804	0.208	135	0.1858	2556	100
2.2804-2.3842	0.2406	134	0.1804	2549	100
2.3842-2.5099	0.2415	135	0.1783	2575	100
2.5099-2.6671	0.2063	135	0.1902	2570	100
2.6671-2.873	0.237	137	0.1855	2594	100
2.873-3.1621	0.2288	137	0.1826	2604	100
3.1621-3.6195	0.2072	137	0.1726	2603	100
3.6195-4.5594	0.1959	140	0.138	2669	100
4.5594-44.5	0.1802	149	0.1563	2807	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	5.2846	-4.5163	-0.6992	8.1715	-3.8051	4.6566	-0.0469	0.0132	-0.1105	0.0012	0.0796	0.1865	-0.1415	-0.1171	-0.074	0.2416	-0.1064	0.0067	0.1346	-0.0401	0.1875	-4.371	35.3403	3.5126
2	3.1232	0.1673	0.1125	5.2768	-4.9601	7.3868	-0.0471	-0.1846	0.1397	0.4646	0.0951	-0.0366	-0.6691	0.0773	-0.0302	0.2639	-0.0583	-0.0014	0.1573	-0.0629	0.1591	-3.6044	39.2561	7.234
3	8.2956	1.9367	5.3367	7.4716	2.5892	4.2344	-0.1857	0.4679	0.9981	-0.432	-0.1048	0.1447	-0.9363	0.0474	0.3401	0.2727	0.0021	0.0394	0.2646	0.0226	0.3313	-8.0213	49.1766	-1.0945
4	3.886	1.9321	-2.8487	5.2567	-3.9433	6.3748	0.1046	0.2043	0.2039	-0.2396	0.2582	0.1519	-0.0899	0.2549	-0.3855	0.2524	-0.0956	-0.0438	0.2246	-0.0119	0.2657	3.4744	46.7329	-7.0565
5	7.0987	-5.2508	4.6146	4.7417	-5.7239	9.5632	0.2177	0.5928	-0.0534	-0.6125	-0.3015	-0.6816	0.2517	0.709	0.1247	0.2834	-0.0696	0.0469	0.339	-0.0385	0.3635	8.9559	34.1216	-1.2893
6	8.0972	-1.2879	-1.6427	5.339	0.9261	3.3651	-0.0469	0.4409	-0.3974	-0.3039	0.1089	-0.4208	0.2004	0.0603	-0.0297	0.2679	-0.0779	0.0082	0.1796	-0.0242	0.2518	0.7561	27.0884	-0.0063
7	5.0408	1.778	-2.9197	7.136	-0.8445	3.6657	0.3705	-0.7041	-0.9402	0.4849	-0.1933	-0.3456	0.8199	0.0876	-0.1983	0.4292	-0.0339	-0.0844	0.3076	0.0967	0.4365	-0.2062	19.7986	12.4236
8	5.1101	2.7053	-1.3451	5.649	-0.67	7.6477	0.0791	-0.1646	-0.2914	0.4111	-0.3625	-0.2994	-0.0595	-0.0565	0.2653	0.2729	-0.1613	-0.0424	0.2918	0.012	0.3219	17.3843	53.2972	0.109
9	3.2271	1.4209	-0.1081	7.1147	1.2612	3.0291	0.3745	-0.3158	-0.4376	0.6014	-0.2899	-1.0894	0.1184	0.2876	-0.0889	0.2894	-0.1504	-0.092	0.3653	0.0667	0.4504	23.0052	52.8389	1.8619
10	7.2552	1.1847	-0.9797	3.8462	-1.6922	3.2712	0.875	-1.3844	0.6042	1.4079	-0.631	-0.3337	-0.8858	0.2889	-0.3865	0.786	-0.4369	-0.0033	0.6764	-0.0143	0.4497	19.9303	61.5653	12.0269
11	9.4833	-3.1985	-0.3937	6.4046	0.4959	4.3382	0.591	-0.3238	0.4733	0.494	-0.4115	0.2879	-0.2258	-0.5769	-0.1798	0.3192	-0.2026	0.0772	0.4326	-0.0189	0.4267	19.9163	70.5416	2.4545
12	3.2232	0.3342	1.6957	4.5514	4.3962	4.8754	-0.2588	0.4306	0.256	-0.2125	-0.2652	-0.0454	-0.5276	-0.1265	0.4544	0.3635	-0.1446	0.0125	0.3656	0.0356	0.3188	20.5121	62.6724	-10.3745
13	4.6946	1.4181	0.938	4.0026	-0.7101	3.2413	-0.181	0.2926	0.1937	-0.3393	0.132	-0.1179	-0.1942	0.0737	0.0699	0.298	-0.1465	0.0276	0.2944	-0.0421	0.2639	14.091	54.0024	-9.5388
14	3.703	-1.1091	3.4163	5.3826	-1.8419	6.4324	0.0756	0.4152	-0.8178	-0.8928	0.2355	-0.8016	0.4994	0.0838	-0.199	0.4119	-0.1061	0.126	0.3435	-0.1595	0.4334	17.0026	41.5878	-13.4781

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 261 through 286 )	A	261 - 286
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 287 through 314 )	A	287 - 314
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 315 through 334 )	A	315 - 334
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 335 through 354 )	A	335 - 354
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 355 through 365 )	A	355 - 365
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 366 through 406 )	A	366 - 406
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 407 through 428 )	A	407 - 428
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 262 through 286 )	B	262 - 286
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 287 through 314 )	B	287 - 314
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 315 through 334 )	B	315 - 334
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 335 through 354 )	B	335 - 354
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 355 through 365 )	B	355 - 365
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 366 through 406 )	B	366 - 406
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 407 through 425 )	B	407 - 425

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