PDB-8gze: Crystal Structure of human METTL9-SAH-SLC39A7 peptide complex

ID or keywords:

Entry

Database: PDB / ID: 8gze

Title

Crystal Structure of human METTL9-SAH-SLC39A7 peptide complex

Components

Protein-L-histidine N-pros-methyltransferase
Zinc transporter SLC39A7

Keywords

TRANSFERASE / DREV domain / Methyltransferase

Function / homology

Function and homology information

regulation of ferroptosis / Zinc influx into cells by the SLC39 gene family / protein-L-histidine N-pros-methyltransferase activity / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / intracellular zinc ion homeostasis / B cell differentiation / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / endoplasmic reticulum membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name ..._pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model
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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Download

PDBx/mmCIF format	8gze.cif.gz	238.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8gze.ent.gz	191.5 KB	Display	PDB format
PDBx/mmJSON format	8gze.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gze_validation.pdf.gz	956.4 KB	Display	wwPDB validaton report
Full document	8gze_full_validation.pdf.gz	963.5 KB	Display
Data in XML	8gze_validation.xml.gz	21.3 KB	Display
Data in CIF	8gze_validation.cif.gz	28 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gz/8gze ftp://data.pdbj.org/pub/pdb/validation_reports/gz/8gze	HTTPS FTP

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Related structure data

Related structure data	8gzfC 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

E: Zinc transporter SLC39A7

D: Zinc transporter SLC39A7

hetero molecules

63.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

D: Zinc transporter SLC39A7

hetero molecules

defined by author&software
Evidence: light scattering
31.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

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

E: Zinc transporter SLC39A7

hetero molecules

defined by author&software
31.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.182, 79.182, 422.365
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#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: Protein/peptide	Zinc transporter SLC39A7 / Histidine-rich membrane protein Ke4 / Really interesting new gene 5 protein / Solute carrier family ...Histidine-rich membrane protein Ke4 / Really interesting new gene 5 protein / Solute carrier family 39 member 7 / Zrt- / Irt-like protein 7 / ZIP7 Mass: 581.578 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92504
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.22 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% w/v PEG 4000, 500 mM KCl.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 3.4→50 Å / Num. obs: 18922 / % possible obs: 92.4 % / Redundancy: 3 % / R_merge(I) obs: 0.966 / Χ²: 0.11 / Net I/σ(I): 3.4 / Num. measured all: 56335

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
3.4-3.46	3.1	0.687	919	0.494	1	89
3.46-3.52	3	0.675	952	0.492	1	94.1
3.52-3.59	3	0.6	946	0.482	1	91.6
3.59-3.66	3	0.515	945	0.482	1	94
3.66-3.74	2.8	0.533	958	0.524	1	92.8
3.74-3.83	2.9	0.408	939	0.565	1	92
3.83-3.92	2.6	0.377	954	0.619	1	93.7
3.92-4.03	2.9	0.304	950	0.633	1	92.4
4.03-4.15	3	0.261	941	0.62	1	92.7
4.15-4.28	2.9	0.217	965	0.669	1	94.4
4.28-4.44	2.7	0.186	920	0.762	1	89.2
4.44-4.61	3	0.165	933	0.813	1	91.8
4.61-4.82	3	0.153	902	0.818	1	90.5
4.82-5.08	3	0.152	919	0.711	1	89.1
5.08-5.4	2.8	0.141	919	0.7	1	89.3
5.4-5.81	2.6	0.139	920	0.584	1	89.9
5.81-6.4	2.9	0.129	937	0.571	1	91.8
6.4-7.32	2.8	0.088	957	0.653	1	92.7
7.32-9.21	3.3	0.069	996	0.822	1	96.8
9.21-50	4	0.057	1050	1.054	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: 3.4→17.28 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3045	1077	9.63 %
R_work	0.2552	-	-
obs	0.26	11178	95.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.4→17.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4422	0	52	0	4474

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4591
X-RAY DIFFRACTION	f_angle_d	0.775	6226
X-RAY DIFFRACTION	f_dihedral_angle_d	24.106	610
X-RAY DIFFRACTION	f_chiral_restr	0.048	674
X-RAY DIFFRACTION	f_plane_restr	0.005	788

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 (%)
3.4-3.55	0.3375	125	0.2998	1198	X-RAY DIFFRACTION	94
3.55-3.73	0.36	139	0.2791	1222	X-RAY DIFFRACTION	96
3.74-3.97	0.3309	133	0.2854	1226	X-RAY DIFFRACTION	95
3.97-4.27	0.3152	122	0.2587	1244	X-RAY DIFFRACTION	97
4.27-4.69	0.3099	116	0.2476	1249	X-RAY DIFFRACTION	95
4.69-5.35	0.282	134	0.2389	1260	X-RAY DIFFRACTION	95
5.35-6.67	0.3809	139	0.2777	1275	X-RAY DIFFRACTION	95
6.68-17.28	0.2349	169	0.2207	1427	X-RAY DIFFRACTION	99

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	0.3171	-0.6174	0.5645	0.9721	-1.2637	1.5464	-0.2308	-0.311	0.5974	0.5382	-0.0475	-0.02	0.1306	0.2252	-0.0003	0.7138	0.0819	-0.0004	0.639	-0.0254	0.4785	-3.4763	-10.658	-1.9257
2	1.1573	0.1193	0.1812	0.0061	-0.018	0.0135	-0.3849	0.7347	-0.0365	-0.3134	0.6611	-1.0276	0.0229	0.2985	-0.0092	0.8606	-0.0154	0.1653	0.5326	0.1026	0.99	-16.7766	-28.2483	-24.3769
3	0.7794	-0.3086	0.2693	0.334	0.148	0.3779	-0.427	0.0433	-0.0622	-0.6706	0.0241	-0.6984	-0.1438	0.0584	-0.0385	0.7958	-0.1719	0.1679	0.6004	0.0821	0.3281	-8.3339	-17.7412	-20.1106
4	0.9739	-0.529	-0.3227	1.4675	-1.1319	1.2305	-0.3301	0.35	0.1826	-0.2319	0.1912	0.4052	0.1101	0.0568	-0.0002	0.7963	-0.0434	0.0299	0.4602	0.0571	0.6124	-0.3088	-2.9118	-22.3294
5	1.7658	-0.7218	0.6569	0.3502	-0.0156	1.3298	0.2759	-0.4133	-0.1794	-0.0657	-0.3046	0.0312	-0.1078	-0.4317	0.0001	0.6251	-0.0794	0.0959	0.5871	0.1626	0.6302	9.3332	-11.7512	-18.4421
6	0.3756	-0.7015	0.4173	1.6207	0.3904	1.3489	-0.2779	0.0917	-0.2093	-0.3369	0.3202	0.288	-0.1184	0.3266	-0	0.6676	0.0885	0.0111	0.6458	0.0786	0.5375	12.0867	-16.2851	-10.1022
7	5.6379	-1.0864	-0.8721	3.9063	0.5141	1.636	0.1676	0.7921	-1.4558	0.0074	-0.6734	1.2753	-0.827	-0.4102	-2.541	0.8165	-0.0663	0.1479	0.2788	0.502	-0.0361	-4.0032	-16.4824	-9.8843
8	1.7609	-0.9599	1.5749	1.7852	-0.7313	1.3957	0.0978	-0.2666	0.5475	0.0121	-0.0011	-0.101	0.3922	0.4296	-0.0001	0.8788	-0.0914	0.2133	0.5107	0.0751	0.8638	-38.2877	-7.4172	6.6598
9	7.5323	1.5025	2.5974	1.5616	0.4805	0.9136	1.4265	1.1974	-1.3297	-0.7195	0.3696	0.1356	-1.3726	-0.1881	0.3598	1.4179	0.0913	0.1557	0.7554	-0.1371	0.8501	-34.1187	-20.9674	-20.9827
10	1.6406	-0.2074	-1.3334	1.0835	-0.0826	1.225	0.5499	-0.8946	-0.0375	0.4836	-0.1962	-0.2955	0.8679	-1.1481	0.0001	0.5399	-0.0752	0.0444	0.6364	0.0626	0.7572	-28.7634	-18.4817	3.1139
11	0.6336	-0.0388	0.0561	1.076	0.703	0.5454	0.0651	0.3591	0.2564	0.5927	0.2579	-0.0164	0.5122	0.5325	-0.0001	0.6688	-0.087	-0.0719	0.6295	-0.0056	0.695	-24.1438	-28.2885	4.7625
12	1.149	-0.6265	-0.9287	1.9944	-0.8321	1.3936	-0.1666	0.2844	-0.1743	0.0044	-0.0518	-0.096	-0.2901	0.3253	-0.0002	0.6689	-0.0162	0.0339	0.6138	-0.0319	0.9252	-37.1852	-27.9876	9.6947
13	0.5945	0.6715	0.1332	0.5947	-0.2131	0.3984	0.2326	0.0761	-0.9128	0.078	0.1751	1.6905	0.2134	-0.4959	-0.0216	0.808	0.1063	0.2007	0.6944	0.1142	0.7746	-48.1937	-25.7758	11.4786
14	1.0091	0.5992	0.7564	1.2666	1.4112	1.3637	0.2081	0.0111	0.2305	0.0104	-0.0157	0.4667	-0.2455	0.4339	-0.0001	0.7304	-0.0453	0.1074	0.4318	0.1106	0.7112	-38.306	-15.8283	5.793
15	1.9599	-1.4667	-1.7358	4.9875	2.199	1.7418	-0.3712	-0.2258	-0.2411	1.1635	1.0636	-0.26	1.3776	-0.1912	0.1099	0.548	-0.1444	0.172	0.6063	-0.0306	0.9085	-40.429	-20.7105	-4.3844
16	1.7557	-1.1592	-1.5795	1.0327	1.7479	3.2955	-0.237	-0.121	-0.1162	-0.3828	0.1461	-1.1163	-0.2156	0.2764	0.3966	1.0486	0.1334	0.1252	-0.0595	0.4251	0.5004	-3.7698	-21.8271	-15.374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 55 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 111 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 130 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 204 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 205 through 251 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 252 through 294 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 295 through 317 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 53 through 94 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 95 through 109 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 110 through 147 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 148 through 204 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 205 through 253 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 254 through 283 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 284 through 318 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 1 through 5 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 5 )

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