7UBU: ZMET2

Crystal structure of ZMET2 in complex with hemimethylated CAG DNA and a histone H3Kc9me2 peptide. Determined by X-ray diffraction at 2.39 Å resolution. Released 8 Jun 2022.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Zea mays
Chains: 5
Atoms: 6,690
Mol. weight: 105.97 kDa
Ligands: SAH
Released: 8 Jun 2022

Explore 7UBU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UBU contains 47 α-helices and 48 β-strands across 3 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: 44 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	136-138	3	1
α-helix	141-143	3
α-helix	144-150	7
α-helix	152-154	3
β-strand	172-176	5	2
β-strand	178-181	4	1
β-strand	184-187	4	1
β-strand	191-194	4	2
α-helix	201-202	2
β-strand	203-213	11	2
β-strand	218-226	9	2
α-helix	227	1
α-helix	228-230	3
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	280-287	8
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	339-346	8	2
α-helix	352-364	13
β-strand	366-374	9	2
α-helix	378-387	10
β-strand	392-394	3	2
α-helix	398-414	17
α-helix	430-431	2
β-strand	432	1	5
α-helix	433	1
β-strand	440-442	3	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	479-482	4
α-helix	486-499	14
α-helix	503-504	2
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	571-582	12
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	635-640	6
β-strand	641	1	2
β-strand	645	1	11
α-helix	646-648	3
α-helix	649-651	3
β-strand	653	1	10
α-helix	654-656	3
α-helix	658-662	5
α-helix	666-667	2
β-strand	676-677	2	12
α-helix	686-691	6
β-strand	714-715	2	12
α-helix	724-731	8
α-helix	741-743	3
β-strand	747-749	3	13
α-helix	751-753	3
β-strand	755-757	3	13
α-helix	762-764	3
β-strand	765	1	14
β-strand	771	1	14
α-helix	775-779	5
β-strand	790-791	2	15
β-strand	798	1	8
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	855-869	15
β-strand	879-880	2	9
α-helix	881-883	3
α-helix	884-886	3

Chain P: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	15-17	3
β-strand	18	1	11

Chain Q: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-8	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 1	A	protein	783	Zea mays	Q9AXT8 (AlphaFold model)
Histone H3.2	P, Q	protein	33	Zea mays	P69246 (AlphaFold model)
5MC ssDNA	B	DNA	18	Zea mays
C49 ssDNA	C	DNA	18	Zea mays

Sequence of entity 1 (A), FASTA

>7UBU_1 DNA (cytosine-5)-methyltransferase 1 (chains A)
AGDHEPEFIGSPVAADEARSNWPKRYGRSTAAKKPDEEEELKARCHYRSAKVDNVVYCLG
DDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDPR
RVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANIS
SENGQSGSDTASGISSDDVDLETSSSMPTRTATLLDLYSGCGGMSTGLCLGAALSGLKLE
TRWAVDFNSFACQSLKYNHPQTEVRNEKADEFLALLKEWAVLCKKYVQDVDSNLASSEDQ
ADEDSPLDKDEFVVEKLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNLSDCPQKI
REFVQEGHKRKILPLPGDVDVICGGPPCQGISGFNRYRNRDEPLKDEKNKQMVTFMDIVA
YLKPKYVLMENVVDILKFADGYLGKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFLW
GALSSMVLPKYPLPTYDVVVRGGAPNAFSQCMVAYDETQKPSLKKALLLGDAISDLPKVQ
NHQPNDVMEYGGSPKTEFQRYIRLSRKDMLDWSFGEGAGPDEGKLLDHQPLRLNNDDYER
VQQIPVKKGANFRDLKGVRVGANNIVEWDPEIERVKLSSGKPLVPDYAMSFIKGKSLKPF
GRLWWDETVPTVVTRAEPHNQVIIHPTQARVLTIRENARLQGFPDYYRLFGPIKEKYIQV
GNAVAVPVARALGYCLGQAYLGESEGSDPLYQLPPSFTSVGGRTAGQARASPVGTPAGEV
VEQ

Sequence of entity 2 (P, Q), FASTA

>7UBU_2 Histone H3.2 (chains P, Q)
SARTKQTARKSTGGKAPRKQLATKAARKSAPAT

Sequence of entity 3 (B), FASTA

>7UBU_3 5MC SSDNA (chains B)
TAAATTCTGATTAGGAAT

Sequence of entity 4 (C), FASTA

>7UBU_4 C49 SSDNA (chains C)
ATTCCTAATCAGAATTTA

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Primary citation

Mechanistic basis for maintenance of CHG DNA methylation in plants. Fang, J., Jiang, J., Leichter, S.M. et al. Nat Commun (2022) 13:3877-3877. DOI 10.1038/s41467-022-31627-3 · PubMed

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

4FT4 2.7 Å, crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH
9MVY 2.71 Å, Crystal structure of ZMET2 in complex with unmethylated CTG DNA and a histone H3Kc9me2…
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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