4FT4: DNA-methyltransferase 1

Name: PDB 4FT4: crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH
Published: 2012-10-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH. Determined by X-ray diffraction at 2.7 Å resolution. Released 17 Oct 2012.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Zea mays
Chains: 4
Atoms: 11,265
Mol. weight: 182.7 kDa
Ligands: SAH
Released: 17 Oct 2012

Explore 4FT4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FT4 contains 78 α-helices and 77 β-strands across 2 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: 38 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	136-138	3	12
α-helix	140-143	4
α-helix	144-150	7
α-helix	152-154	3
β-strand	172-176	5	13
β-strand	178-181	4	12
β-strand	184-187	4	12
β-strand	191-194	4	13
α-helix	201-202	2
β-strand	203-213	11	13
β-strand	218-226	9	13
α-helix	227	1
α-helix	228-230	3
β-strand	241	1	14
β-strand	244	1	14
β-strand	250-261	12	13
α-helix	262-264	3
β-strand	265-268	4	13
β-strand	271-273	3	13
α-helix	280-288	9
β-strand	292-296	5	13
β-strand	297-299	3	15
α-helix	301-303	3
β-strand	304-306	3	15
β-strand	340-346	7	15
α-helix	352-364	13
β-strand	367-375	9	15
α-helix	378-387	10
β-strand	392-395	4	15
α-helix	398-414	17
β-strand	443-451	9	16
β-strand	460-466	7	16
α-helix	471-473	3
β-strand	475-477	3	16
α-helix	486-498	13
β-strand	510-513	4	15
α-helix	522-524	3
α-helix	532-535	4
α-helix	540-551	12
β-strand	555-561	7	15
α-helix	563-582	20
β-strand	585-593	9	15
α-helix	594-597	4
β-strand	604-612	9	15
α-helix	616-618	3
β-strand	620-621	2	17
α-helix	622-623	2
β-strand	625-626	2	18
α-helix	634	1
α-helix	638-640	3
β-strand	641	1	15
β-strand	653-654	2	18
α-helix	655-657	3
α-helix	658-662	5
α-helix	666-667	2
β-strand	676-677	2	19
α-helix	686-691	6
β-strand	714-715	2	19
α-helix	722-723	2
α-helix	727-731	5
α-helix	741-743	3
α-helix	751-753	3
α-helix	762-764	3
β-strand	765	1	20
β-strand	771	1	20
α-helix	775-779	5
β-strand	790-791	2	21
β-strand	811-813	3	21
β-strand	820	1	21
α-helix	821-822	2
α-helix	823-829	7
α-helix	842-851	10
α-helix	853-854	2
α-helix	855-870	16
β-strand	879-880	2	17

Chain B: 40 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	136-137	2	1
α-helix	141-143	3
α-helix	144-150	7
α-helix	152-154	3
β-strand	172-175	4	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	218-227	10	2
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	251-261	11	2
α-helix	262-264	3
β-strand	265-268	4	2
β-strand	271-273	3	4
α-helix	280-289	10
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	366-375	10	2
α-helix	378-387	10
β-strand	392-395	4	2
α-helix	398-414	17
β-strand	443-451	9	5
α-helix	457	1
β-strand	460-466	7	5
β-strand	475-478	4	5
α-helix	480-482	3
α-helix	486-499	14
β-strand	510-513	4	2
α-helix	522-526	5
α-helix	539-551	13
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	604-611	8	2
α-helix	616-618	3
β-strand	620-621	2	6
α-helix	622-623	2
β-strand	625	1	7
α-helix	635-637	3
β-strand	641	1	2
β-strand	653	1	7
α-helix	654-656	3
α-helix	658-662	5
α-helix	666-667	2
β-strand	676-677	2	8
α-helix	686-691	6
β-strand	714-715	2	8
α-helix	724-732	9
α-helix	741-743	3
β-strand	747-749	3	9
α-helix	751-753	3
β-strand	755-757	3	9
α-helix	762-764	3
β-strand	765	1	10
β-strand	771	1	10
α-helix	775-779	5
α-helix	780-783	4
β-strand	790-791	2	11
α-helix	792	1
β-strand	811-813	3	11
β-strand	820	1	11
α-helix	821-822	2
α-helix	823-829	7
α-helix	842-851	10
α-helix	853-854	2
α-helix	855-870	16
β-strand	879-880	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 1	A, B	protein	784	Zea mays	Q9AXT8 (AlphaFold model)
H3(1-32)K9me2 peptide	P, Q	protein	32		P59226 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4FT4_1 DNA (cytosine-5)-methyltransferase 1 (chains A, B)
SAGDHEPEFIGSPVAADEARSNWPKRYGRSTAAKKPDEEEELKARCHYRSAKVDNVVYCL
GDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDP
RRVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANI
SSENGQSGSDTASGISSDDVDLETSSSMPTRTATLLDLYSGCGGMSTGLCLGAALSGLKL
ETRWAVDFNSFACQSLKYNHPQTEVRNEKADEFLALLKEWAVLCKKYVQDVDSNLASSED
QADEDSPLDKDEFVVEKLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNLSDCPQK
IREFVQEGHKRKILPLPGDVDVICGGPPCQGISGFNRYRNRDEPLKDEKNKQMVTFMDIV
AYLKPKYVLMENVVDILKFADGYLGKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFL
WGALSSMVLPKYPLPTYDVVVRGGAPNAFSQCMVAYDETQKPSLKKALLLGDAISDLPKV
QNHQPNDVMEYGGSPKTEFQRYIRLSRKDMLDWSFGEGAGPDEGKLLDHQPLRLNNDDYE
RVQQIPVKKGANFRDLKGVRVGANNIVEWDPEIERVKLSSGKPLVPDYAMSFIKGKSLKP
FGRLWWDETVPTVVTRAEPHNQVIIHPTQARVLTIRENARLQGFPDYYRLFGPIKEKYIQ
VGNAVAVPVARALGYCLGQAYLGESEGSDPLYQLPPSFTSVGGRTAGQARASPVGTPAGE
VVEQ

Sequence of entity 2 (P, Q), FASTA

>4FT4_2 H3(1-32)K9me2 peptide (chains P, Q)
ARTKQTARKSTGGKAPRKQLATKAARKSAPAT

Ligands and cofactors

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

Primary citation

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants. Du, J., Zhong, X., Bernatavichute, Y.V. et al. Cell (2012) 151:167-180. DOI 10.1016/j.cell.2012.07.034 · 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…
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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