9MVY: ZMET2

Name: PDB 9MVY: Crystal structure of ZMET2 in complex with unmethylated CTG DNA and a histone H3Kc9me2 peptide
Published: 2025-05-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of ZMET2 in complex with unmethylated CTG DNA and a histone H3Kc9me2 peptide. Determined by X-ray diffraction at 2.71 Å resolution. Released 21 May 2025.

Method: X-ray diffraction
Resolution: 2.71 Å
Organisms: Zea mays, synthetic construct
Chains: 10
Atoms: 13,299
Mol. weight: 206.8 kDa
Ligands: SAH
Released: 21 May 2025

Explore 9MVY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MVY contains 79 α-helices and 92 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 39 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	136-138	3	1
α-helix	140-143	4
α-helix	144-150	7
β-strand	172-176	5	2
β-strand	178-180	3	1
β-strand	185-187	3	1
β-strand	191-194	4	2
α-helix	200-202	3
β-strand	203-213	11	2
β-strand	218-226	9	2
α-helix	227	1
α-helix	234-238	5
β-strand	241	1	3
β-strand	244	1	3
β-strand	250	1	4
β-strand	252-261	10	2
α-helix	262-264	3
β-strand	265-268	4	2
β-strand	271-273	3	4
α-helix	280-282	3
α-helix	284-287	4
β-strand	292-294	3	4
β-strand	296-299	4	2
α-helix	301-303	3
β-strand	304-307	4	2
β-strand	340-341	2	5
β-strand	343-346	4	2
α-helix	352-364	13
β-strand	367-368	2	5
β-strand	372-374	3	2
α-helix	378-387	10
β-strand	392-394	3	2
α-helix	398-414	17
β-strand	441	1	6
β-strand	443-451	9	7
β-strand	460-466	7	7
α-helix	471-473	3
β-strand	475-478	4	7
α-helix	486-498	13
β-strand	510-513	4	2
α-helix	536-551	16
β-strand	555-561	7	2
α-helix	562-565	4
α-helix	567-570	4
α-helix	571-581	11
β-strand	586-593	8	2
α-helix	594-597	4
β-strand	601	1	8
β-strand	604-611	8	2
α-helix	616-618	3
β-strand	620-621	2	9
α-helix	622-623	2
β-strand	625	1	10
α-helix	638-640	3
β-strand	641	1	2
β-strand	644-645	2	11
α-helix	652	1
β-strand	653	1	10
α-helix	654-656	3
α-helix	659-662	4
α-helix	666-667	2
β-strand	676-677	2	12
α-helix	686-691	6
α-helix	696-698	3
β-strand	714-715	2	12
α-helix	724-732	9
α-helix	741-743	3
β-strand	747-749	3	13
α-helix	751-753	3
β-strand	755-757	3	13
β-strand	765	1	14
β-strand	771	1	14
α-helix	775-783	9
β-strand	790-791	2	15
α-helix	792	1
β-strand	798	1	8
α-helix	807-809	3
β-strand	811-813	3	15
β-strand	820	1	15
α-helix	821-822	2
α-helix	823-829	7
α-helix	842-851	10
α-helix	855-870	16
β-strand	879-880	2	9
α-helix	881-884	4

Chain D: 39 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	136-138	3	16
α-helix	140-143	4
α-helix	144-150	7
β-strand	172-176	5	17
β-strand	178-181	4	16
β-strand	184-187	4	16
β-strand	191-194	4	17
α-helix	200-202	3
β-strand	203-213	11	17
β-strand	218-226	9	17
α-helix	227	1
α-helix	234-238	5
β-strand	240-241	2	18
β-strand	244-245	2	18
β-strand	250	1	19
β-strand	252-261	10	17
α-helix	262-264	3
β-strand	265-268	4	17
β-strand	271-273	3	19
α-helix	282-288	7
β-strand	292-294	3	19
β-strand	296-299	4	17
α-helix	301-303	3
β-strand	304-307	4	17
β-strand	339-346	8	17
α-helix	352-364	13
β-strand	366-375	10	17
α-helix	378-387	10
β-strand	392-395	4	17
α-helix	398-414	17
α-helix	441-442	2
β-strand	443-451	9	20
β-strand	460-466	7	20
β-strand	475-478	4	20
α-helix	486-499	14
α-helix	503-504	2
β-strand	510-513	4	17
α-helix	536-551	16
β-strand	555-561	7	17
α-helix	562-565	4
α-helix	567-570	4
α-helix	571-582	12
β-strand	586-593	8	17
α-helix	594-597	4
β-strand	601	1	21
β-strand	604-611	8	17
α-helix	617-619	3
β-strand	620-621	2	22
α-helix	622-623	2
β-strand	625	1	23
α-helix	635-640	6
β-strand	641	1	17
β-strand	645	1	24
β-strand	653	1	23
α-helix	654-656	3
α-helix	659-662	4
α-helix	666-667	2
β-strand	676-677	2	25
α-helix	686-691	6
α-helix	696-698	3
β-strand	714-715	2	25
α-helix	724-731	8
α-helix	741-743	3
β-strand	747-749	3	26
α-helix	751-753	3
β-strand	755-757	3	26
β-strand	765	1	27
β-strand	771	1	27
α-helix	775-779	5
α-helix	780-783	4
β-strand	790-791	2	28
β-strand	798	1	21
β-strand	811-813	3	28
β-strand	820	1	28
α-helix	821-822	2
α-helix	823-829	7
α-helix	842-850	9
α-helix	853-854	2
α-helix	855-870	16
β-strand	879-880	2	22
α-helix	881-883	3
α-helix	884-886	3

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	18	1	24

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	6

Chain P: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-17	2
β-strand	18-19	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 1	A, D	protein	758	Zea mays	Q9AXT8 (AlphaFold model)
ssDNA	B, E	DNA	18	synthetic construct
C49 ssDNA	C, F	DNA	18	synthetic construct
Histone H3.2	G, H, I, P	protein	32	Zea mays	P69246 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9MVY_1 DNA (cytosine-5)-methyltransferase 1 (chains A, D)
AGDHEPEFIGSPVAADEARSNWPKRYGRSTAAKKPDEEEELKARCHYRSAKVDNVVYCLG
DDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDPR
RVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANIS
SENGQSGSDTASGISSDDVDLETSSSMPTRTATLLDLYSGCGGMSTGLCLGAALSGLKLE
TRWAVDFNSFACQSLKYNHPQTEVRNEKADEFLALLKEWAVLCKKYVQDVDSNLASSEDQ
ADEDSPLDKDEFVVEKLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNLSDCPQKI
REFVQEGHKRKILPLPGDVDVICGGPPCQGISGFNRYRNRDEPLKDEKNKQMVTFMDIVA
YLKPKYVLMENVVDILKFADGYLGKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFLW
GALSSMVLPKYPLPTYDVVVRGGAPNAFSQCMVAYDETQKPSLKKALLLGDAISDLPKVQ
NHQPNDVMEYGGSPKTEFQRYIRLSRKDMLDWSFGEGAGPDEGKLLDHQPLRLNNDDYER
VQQIPVKKGANFRDLKGVRVGANNIVEWDPEIERVKLSSGKPLVPDYAMSFIKGKSLKPF
GRLWWDETVPTVVTRAEPHNQVIIHPTQARVLTIRENARLQGFPDYYRLFGPIKEKYIQV
GNAVAVPVARALGYCLGQAYLGESEGSDPLYQLPPSFT

Sequence of entity 2 (B, E), FASTA

>9MVY_2 ssDNA (chains B, E)
TAAATTCAGATTAGGAAT

Sequence of entity 3 (C, F), FASTA

>9MVY_3 C49 ssDNA (chains C, F)
ATTCCTAATCTGAATTTA

Sequence of entity 4 (G, H, I, P), FASTA

>9MVY_4 Histone H3.2 (chains G, H, I, P)
ARTKQTARKSTGGKAPRKQLATKAARKSAPAT

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2. Herle, G., Fang, J., Song, J. J Mol Biol (2025) 437:169186-169186. DOI 10.1016/j.jmb.2025.169186 · PubMed

Other PDB entries of the same protein (UniProt Q9AXT8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UBU 2.39 Å, Crystal structure of ZMET2 in complex with hemimethylated CAG DNA and a histone H3Kc9me2…
4FT4 2.7 Å, crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH
4FSX 3.2 Å, crystal structure of Se-substituted Zea mays ZMET2 in complex with SAH
4FT2 3.2 Å, crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH

Browse structure collections

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