4FSX: Se-substituted Zea mays ZMET2

crystal structure of Se-substituted Zea mays ZMET2 in complex with 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: 2
Atoms: 10,631
Mol. weight: 177.45 kDa
Ligands: SAH
Released: 17 Oct 2012

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

Secondary structure: helices and β-sheets

4FSX contains 62 α-helices and 72 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: 30 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
α-helix	201-202	2
β-strand	203-212	10	1
β-strand	218-226	9	1
α-helix	228-230	3
α-helix	236-238	3
β-strand	240-241	2	3
β-strand	244-245	2	3
β-strand	251-261	11	1
β-strand	268-269	2	1
β-strand	271-273	3	1
α-helix	282-288	7
β-strand	292-299	8	1
β-strand	304-307	4	1
β-strand	339-346	8	4
α-helix	352-364	13
β-strand	366-374	9	4
α-helix	378-387	10
β-strand	392-394	3	4
α-helix	398-416	19
β-strand	443-451	9	5
β-strand	460-466	7	5
α-helix	471-473	3
β-strand	475-478	4	5
α-helix	486-499	14
β-strand	504	1	6
β-strand	507	1	6
β-strand	511-513	3	4
α-helix	539-551	13
β-strand	557-561	5	4
α-helix	562-565	4
α-helix	571-582	12
β-strand	585	1	7
β-strand	587	1	1
β-strand	588-593	6	4
α-helix	595-597	3
β-strand	601	1	8
β-strand	604-609	6	4
β-strand	612	1	7
β-strand	620-621	2	9
α-helix	622-623	2
α-helix	654-656	3
α-helix	658-662	5
β-strand	677	1	10
α-helix	686-691	6
α-helix	695-698	4
α-helix	707-708	2
β-strand	714	1	10
α-helix	720-723	4
α-helix	724-732	9
α-helix	775-779	5
α-helix	780-782	3
β-strand	787	1	11
β-strand	791	1	12
β-strand	798	1	8
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	855-869	15
β-strand	879-880	2	9

Chain B: 32 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	136	1	13
β-strand	142	1	14
α-helix	147-150	4
α-helix	152-154	3
β-strand	172-175	4	15
β-strand	176	1	14
β-strand	178-181	4	13
β-strand	184-187	4	13
β-strand	191-194	4	15
β-strand	203-213	11	15
β-strand	218-227	10	15
α-helix	228-230	3
β-strand	251-261	11	15
α-helix	262-264	3
β-strand	265	1	15
β-strand	271-273	3	16
α-helix	276-278	3
α-helix	279-289	11
β-strand	292-294	3	16
β-strand	296-299	4	15
β-strand	304-307	4	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	393-395	3	15
α-helix	398-414	17
β-strand	443-446	4	17
β-strand	450-451	2	18
β-strand	460-463	4	18
β-strand	464-466	3	17
β-strand	476-478	3	18
α-helix	481-483	3
α-helix	486-499	14
β-strand	510-512	3	15
α-helix	539-551	13
β-strand	555-561	7	15
α-helix	563-566	4
α-helix	571-582	12
β-strand	586-593	8	15
α-helix	595-597	3
β-strand	604-611	8	15
β-strand	620-621	2	19
α-helix	622-623	2
β-strand	625	1	20
α-helix	627-629	3
β-strand	641	1	15
α-helix	648-649	2
α-helix	652	1
β-strand	653	1	20
α-helix	654-656	3
α-helix	658-662	5
α-helix	666-667	2
β-strand	676-677	2	21
α-helix	686-691	6
β-strand	714-715	2	21
α-helix	724-731	8
α-helix	741-743	3
α-helix	762-764	3
α-helix	774-779	6
α-helix	780-782	3
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	19

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>4FSX_1 DNA (cytosine-5)-methyltransferase 1 (chains A, B)
SAGDHEPEFIGSPVAADEARSNWPKRYGRSTAAKKPDEEEELKARCHYRSAKVDNVVYCL
GDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDP
RRVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANI
SSENGQSGSDTASGISSDDVDLETSSSMPTRTATLLDLYSGCGGMSTGLCLGAALSGLKL
ETRWAVDFNSFACQSLKYNHPQTEVRNEKADEFLALLKEWAVLCKKYVQDVDSNLASSED
QADEDSPLDKDEFVVEKLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNLSDCPQK
IREFVQEGHKRKILPLPGDVDVICGGPPCQGISGFNRYRNRDEPLKDEKNKQMVTFMDIV
AYLKPKYVLMENVVDILKFADGYLGKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFL
WGALSSMVLPKYPLPTYDVVVRGGAPNAFSQCMVAYDETQKPSLKKALLLGDAISDLPKV
QNHQPNDVMEYGGSPKTEFQRYIRLSRKDMLDWSFGEGAGPDEGKLLDHQPLRLNNDDYE
RVQQIPVKKGANFRDLKGVRVGANNIVEWDPEIERVKLSSGKPLVPDYAMSFIKGKSLKP
FGRLWWDETVPTVVTRAEPHNQVIIHPTQARVLTIRENARLQGFPDYYRLFGPIKEKYIQ
VGNAVAVPVARALGYCLGQAYLGESEGSDPLYQLPPSFTSVGGRTAGQARASPVGTPAGE
VVEQ

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…
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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