5VAH: ATXR5 SET domain

Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26. Determined by X-ray diffraction at 2.4 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Ricinus communis, Arabidopsis thaliana
Chains: 4
Atoms: 3,640
Mol. weight: 56.04 kDa
Ligands: SAH
Released: 5 Apr 2017

Explore 5VAH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VAH contains 20 α-helices and 49 β-strands across 4 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	162	1	1
α-helix	170-186	17
β-strand	190-191	2	2
β-strand	195-196	2	3
α-helix	204-206	3
α-helix	209-211	3
β-strand	212	1	4
α-helix	217	1
β-strand	218	1	5
α-helix	219-220	2
α-helix	221-236	16
β-strand	242-247	6	6
β-strand	251-256	6	6
β-strand	260	1	7
β-strand	264	1	1
β-strand	265-268	4	5
β-strand	271-275	5	3
α-helix	276-278	3
β-strand	288-291	4	3
β-strand	293	1	4
β-strand	300-303	4	3
β-strand	307-308	2	2
α-helix	310-313	4
β-strand	315-316	2	8
α-helix	324-327	4
β-strand	330-337	8	5
β-strand	340-347	8	5
β-strand	351	1	7
α-helix	355	1
β-strand	356	1	6
α-helix	357	1
β-strand	358-359	2	8
β-strand	362	1	9

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	162	1	10
α-helix	170-186	17
β-strand	190-191	2	11
β-strand	195-196	2	12
α-helix	209-211	3
β-strand	212	1	13
β-strand	218	1	14
α-helix	221-236	16
β-strand	242-247	6	15
β-strand	251-256	6	15
β-strand	260	1	16
β-strand	264	1	10
β-strand	265-268	4	14
β-strand	271-275	5	12
α-helix	276-278	3
β-strand	287-291	5	12
β-strand	293	1	13
α-helix	296-298	3
β-strand	300-303	4	12
β-strand	307-308	2	11
α-helix	310-313	4
β-strand	315-316	2	17
α-helix	324-327	4
β-strand	330-337	8	14
β-strand	340-347	8	14
β-strand	351	1	16
α-helix	355	1
β-strand	356	1	15
α-helix	357	1
β-strand	358-359	2	17
β-strand	362	1	18
β-strand	367	1	12

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	3
β-strand	28	1	9

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	12
β-strand	28	1	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable Histone-lysine N-methyltransferase ATXR5	A, B	protein	229	Ricinus communis	B9RU15 (AlphaFold model)
Histone H3.2	C, D	protein	15	Arabidopsis thaliana	P59226 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VAH_1 Probable Histone-lysine N-methyltransferase ATXR5 (chains A, B)
RRRSGSLVYQKRRRRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRS
ANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTF
IAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSSSLVICPDKRGNIARFISGINNHTLDAK
KKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV

Sequence of entity 2 (C, D), FASTA

>5VAH_2 Histone H3.2 (chains C, D)
ATKAARKSAPATGGV

Ligands and cofactors

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

Primary citation

Molecular basis for the methylation specificity of ATXR5 for histone H3. Bergamin, E., Sarvan, S., Malette, J. et al. Nucleic Acids Res (2017) 45:6375-6387. DOI 10.1093/nar/gkx224 · PubMed

Other PDB entries of the same protein (UniProt B9RU15 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
4O30 2.1 Å, Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy
5VBC 2.1 Å, Crystal structure of ATXR5 in complex with histone H3.1
5VA6 2.4 Å, Crystal structure of ATXR5 in complex with histone H3.1 mono-methylated on R26

Browse structure collections

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