4FT2: DNA-methyltransferase 1

Name: PDB 4FT2: crystal structure of Zea mays ZMET2 in complex H3(1-15)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(1-15)K9me2 peptide and SAH. Determined by X-ray diffraction at 3.2 Å resolution. Released 17 Oct 2012.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Zea mays
Chains: 3
Atoms: 10,657
Mol. weight: 177.55 kDa
Ligands: SAH
Released: 17 Oct 2012

Explore 4FT2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FT2 contains 61 α-helices and 77 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: 27 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	147-150	4
β-strand	174-175	2	1
β-strand	178-181	4	2
β-strand	184-187	4	2
β-strand	191-194	4	1
β-strand	203-213	11	1
β-strand	216-226	11	1
β-strand	241	1	3
β-strand	244	1	3
β-strand	252-261	10	1
β-strand	267-268	2	1
β-strand	271-273	3	4
α-helix	282-288	7
β-strand	292-294	3	4
β-strand	296-299	4	1
β-strand	304-307	4	1
β-strand	341-346	6	5
α-helix	352-364	13
β-strand	368-375	8	5
α-helix	378-387	10
β-strand	392-395	4	5
α-helix	398-414	17
β-strand	445-451	7	6
β-strand	460-465	6	6
β-strand	466	1	7
β-strand	469	1	7
α-helix	471-473	3
β-strand	475-478	4	6
α-helix	486-499	14
β-strand	510-513	4	5
α-helix	539-551	13
β-strand	556-561	6	5
α-helix	563-566	4
α-helix	571-582	12
β-strand	585	1	8
β-strand	587	1	1
β-strand	588-593	6	5
β-strand	601	1	9
β-strand	604-609	6	5
β-strand	612	1	8
α-helix	616-618	3
β-strand	620-621	2	10
α-helix	622-623	2
α-helix	654-656	3
α-helix	658-662	5
β-strand	677	1	11
α-helix	686-691	6
α-helix	695-698	4
α-helix	707-708	2
β-strand	714	1	11
α-helix	720-723	4
α-helix	724-732	9
α-helix	775-779	5
α-helix	780-783	4
β-strand	791	1	12
β-strand	798	1	9
α-helix	807-810	4
β-strand	813	1	12
β-strand	820	1	12
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	10

Chain B: 34 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	136	1	13
α-helix	147-150	4
α-helix	152-154	3
β-strand	172-176	5	14
β-strand	178-181	4	13
β-strand	184-187	4	13
β-strand	191-194	4	14
α-helix	202	1
β-strand	203-213	11	14
β-strand	218-227	10	14
β-strand	251-261	11	14
α-helix	262-264	3
β-strand	265-268	4	14
β-strand	271-273	3	15
α-helix	276-278	3
α-helix	282-289	8
β-strand	292-294	3	15
β-strand	296	1	14
β-strand	297-299	3	16
β-strand	304-306	3	16
β-strand	340-346	7	16
α-helix	352-364	13
β-strand	367-375	9	16
α-helix	378-387	10
β-strand	392-395	4	16
α-helix	398-414	17
β-strand	441	1	17
β-strand	443-451	9	18
α-helix	456-457	2
β-strand	460-466	7	18
β-strand	476-478	3	18
α-helix	479-484	6
α-helix	486-499	14
β-strand	510-512	3	16
α-helix	539-551	13
β-strand	555-560	6	16
α-helix	563-566	4
α-helix	567-569	3
α-helix	571-582	12
β-strand	586-593	8	16
α-helix	595-597	3
β-strand	601	1	19
β-strand	604-611	8	16
β-strand	620-621	2	20
α-helix	622-623	2
β-strand	625	1	21
α-helix	627-629	3
β-strand	641	1	16
β-strand	653	1	21
α-helix	654-656	3
α-helix	658-662	5
α-helix	666-667	2
β-strand	676-677	2	22
α-helix	686-691	6
α-helix	707-708	2
β-strand	714-715	2	22
α-helix	720-723	4
α-helix	724-732	9
β-strand	740	1	23
α-helix	741-743	3
α-helix	762-764	3
α-helix	774-777	4
β-strand	790	1	23
β-strand	791	1	24
β-strand	798	1	19
α-helix	807-810	4
β-strand	813	1	24
α-helix	823-829	7
α-helix	842-851	10
α-helix	852-854	3
α-helix	855-870	16
β-strand	879-880	2	20

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 1	A, B	protein	784	Zea mays	Q9AXT8 (AlphaFold model)
H3 peptide	P	protein	15		P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4FT2_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), FASTA

>4FT2_2 H3 peptide (chains P)
ARTKQTARKSTGGKA

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…
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

Browse structure collections

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