PDB-8gzf: Crystal Structure of METTL9-SAH

ID or keywords:

Entry

Database: PDB / ID: 8gzf

Title

Crystal Structure of METTL9-SAH

Components

Protein-L-histidine N-pros-methyltransferase

Keywords

TRANSFERASE / DREV domain / methyltransferase

Function / homology

Function and homology information

protein-L-histidine N-pros-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / endoplasmic reticulum / mitochondrion
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Zhao, W.T. / Li, H.T.

Funding support

China, 1items

Citation

Journal: Cell Insight / Year: 2023
Title: Molecular basis for protein histidine N1-specific methylation of the "His-x-His" motifs by METTL9.
Authors: Zhao, W. / Zhou, Y. / Li, C. / Bi, Y. / Wang, K. / Ye, M. / Li, H.

History

Deposition	Sep 26, 2022	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type
Revision 1.2	Dec 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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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PDBx/mmCIF format	8gzf.cif.gz	237.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8gzf_validation.pdf.gz	989.9 KB	Display	wwPDB validaton report
Full document	8gzf_full_validation.pdf.gz	994 KB	Display
Data in XML	8gzf_validation.xml.gz	21.7 KB	Display
Data in CIF	8gzf_validation.cif.gz	29.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gz/8gzf ftp://data.pdbj.org/pub/pdb/validation_reports/gz/8gzf	HTTPS FTP

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Related structure data

Related structure data	8gzeC 7ezgS 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: Protein-L-histidine N-pros-methyltransferase

B: Protein-L-histidine N-pros-methyltransferase

hetero molecules

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

1

A: Protein-L-histidine N-pros-methyltransferase

hetero molecules

defined by author
Evidence: light scattering
31.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein-L-histidine N-pros-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.807, 109.807, 120.344
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Protein-L-histidine N-pros-methyltransferase / DORA reverse strand protein / DREV / DREV1 / Methyltransferase-like protein 9 / hMETTL9 Mass: 30953.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL9, DREV, CGI-81 / Plasmid: pGex-6p / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9H1A3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Fragment: SAH / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.39 Å³/Da / Density % sol: 63.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4% v/v glycerol, 1.8 M NaCl

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL02U1 / Wavelength: 0.9792 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 25, 2021 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.5→50 Å / Num. obs: 55801 / % possible obs: 100 % / Redundancy: 8.6 % / R_merge(I) obs: 0.998 / Χ²: 0.038 / Net I/σ(I): 7.8 / Num. measured all: 482311

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.5-2.54	9	0.919	2752	0.46	1	100
2.54-2.59	9	0.822	2728	0.456	1	100
2.59-2.64	9	0.702	2831	0.466	1	100
2.64-2.69	9	0.589	2783	0.49	1	100
2.69-2.75	8.9	0.486	2855	0.506	1	100
2.75-2.82	8.8	0.4	2772	0.557	1	100
2.82-2.89	8.7	0.345	2774	0.583	1	100
2.89-2.96	8.6	0.291	2827	0.63	1	100
2.96-3.05	8	0.248	2729	0.692	1	100
3.05-3.15	8.2	0.198	2812	0.817	1	100
3.15-3.26	8.8	0.174	2808	1.019	1	100
3.26-3.39	8.2	0.138	2806	1.366	1	100
3.39-3.55	8.9	0.116	2770	1.702	1	100
3.55-3.73	9.1	0.105	2821	1.963	1	100
3.73-3.97	9	0.093	2775	2.291	1	100
3.97-4.27	8.8	0.081	2781	2.602	1	100
4.27-4.7	8.5	0.074	2782	2.969	1	100
4.7-5.38	8.2	0.074	2817	2.983	1	100
5.38-6.78	7.9	0.073	2810	2.923	1	100
6.78-50	8.4	0.063	2768	3.721	1	99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
MOLREP		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7EZG

7ezg

Resolution: 2.5→28.68 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 25.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2409	1416	5 %
R_work	0.1902	-	-
obs	0.1928	28299	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→28.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4368	0	52	105	4525

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4536
X-RAY DIFFRACTION	f_angle_d	0.566	6156
X-RAY DIFFRACTION	f_dihedral_angle_d	23.964	1674
X-RAY DIFFRACTION	f_chiral_restr	0.042	668
X-RAY DIFFRACTION	f_plane_restr	0.004	780

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 (%)
2.5-2.59	0.2641	116	0.2334	2650	X-RAY DIFFRACTION	100
2.59-2.7	0.2585	157	0.2194	2678	X-RAY DIFFRACTION	100
2.7-2.82	0.254	135	0.211	2707	X-RAY DIFFRACTION	100
2.82-2.97	0.2471	147	0.214	2684	X-RAY DIFFRACTION	100
2.97-3.15	0.3126	146	0.2243	2660	X-RAY DIFFRACTION	100
3.16-3.4	0.2708	144	0.2142	2692	X-RAY DIFFRACTION	100
3.4-3.74	0.2564	158	0.1867	2669	X-RAY DIFFRACTION	100
3.74-4.28	0.2324	139	0.1797	2685	X-RAY DIFFRACTION	100
4.28-5.38	0.2154	126	0.1688	2724	X-RAY DIFFRACTION	100
5.39-28.68	0.2155	148	0.1799	2734	X-RAY DIFFRACTION	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	0.2135	-0.2134	0.0104	0.3555	0.0579	0.1115	-0.0575	0.2675	0.1387	-0.1113	-0.3061	-0.3446	-0.4773	0.4617	-0.0692	0.6788	-0.3985	0.0348	0.6306	-0.1839	0.8752	31.6446	44.1632	11.8014
2	-0.0152	0.0146	0.0152	0.0193	-0.0066	0.0479	0.1416	-0.1342	0.0245	-0.0941	-0.0349	-0.1655	0.0642	0.1355	0.0001	0.3286	0.0091	0.02	0.435	-0.0594	0.4232	16.9056	17.762	6.522
3	0.1838	-0.1039	-0.2411	0.2873	0.0901	0.2131	0.0397	-0.2972	-0.056	0.3839	0.0079	-0.1219	-0.0193	0.1817	0.0107	0.4079	-0.0573	-0.1079	0.4804	-0.0678	0.3601	17.7511	27.3103	25.1347
4	0.1079	0.0918	-0.0093	0.3134	0.038	0.0435	0.0417	-0.1056	0.5008	0.046	0.0338	0.1764	-0.55	-0.0104	0.085	0.6521	-0.0772	-0.0903	0.4975	-0.2036	0.4477	12.0363	39.548	23.206
5	0.3279	-0.0795	0.2301	0.657	0.0138	0.2563	0.0632	-0.009	0.4349	-0.2193	-0.2879	-0.3155	-0.5102	0.3825	-0.3987	0.6562	-0.2347	-0.1283	0.414	-0.1299	0.5816	20.546	41.6836	14.6905
6	0.3301	0.2329	0.0512	0.2169	-0.0014	0.0794	0.1063	-0.2589	0.4145	0.1604	-0.0986	-0.1329	-0.4269	-0.1128	-0.0381	0.8685	0.2968	-0.186	0.4435	-0.042	0.9894	-4.97	53.9859	-12.1846
7	0.0245	0.0438	0.055	0.0333	0.0585	0.0689	0.2048	-0.1812	0.0589	-0.2861	0	0.0473	0.0826	-0.2572	0	0.3133	0.0603	-0.0189	0.5239	0.0528	0.4457	-5.4943	23.8232	-7.0105
8	0.0072	-0.0298	-0.0121	0.0029	-0.0246	0.0299	-0.1628	0.1391	0.1706	-0.0861	-0.0012	0.0703	0.0169	-0.0358	-0.0001	0.4053	0.1504	-0.0544	0.4536	0.016	0.3889	1.2611	26.8453	-14.4586
9	0.4266	-0.1163	0.1316	0.1751	0.034	0.2065	-0.0535	0.8714	0.2565	-0.3398	-0.068	0.2845	-0.1237	-0.0161	-0.007	0.6212	0.1624	-0.0774	0.6174	0.2405	0.5028	-3.0323	33.7242	-28.5064
10	0.1461	-0.133	-0.0495	0.2096	0.0374	0.0067	0.048	0.3557	0.626	-0.3278	0.0134	-0.5651	-0.3519	0.262	0.2217	0.6164	0.0778	0.0426	0.7839	0.5107	0.763	7.0965	41.4218	-29.7263
11	0.0154	0	0.0185	0.0029	0.0133	0.0007	-0.2972	-0.145	0.0883	-0.0028	-0.0835	-0.0187	0.2671	0.3966	0.0001	0.8483	0.0101	-0.1292	0.8974	0.1844	1.2463	15.7663	36.3689	-12.7673
12	0.511	-0.0429	0.3564	0.2241	0.0923	0.3199	-0.4311	-0.4267	1.1241	0.1118	-0.231	-0.3622	-0.4123	-0.0279	-0.5469	0.6459	0.0456	-0.3319	0.1164	0.287	1.1488	3.3886	46.4032	-15.3682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 53 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 110 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 261 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 262 through 318 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 53 through 78 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 79 through 110 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 111 through 130 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 131 through 195 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 196 through 241 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 242 through 261 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 262 through 318 )

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