6AGO: MRG15-ASH1L Histone methyltransferase complex

Crystal structure of MRG15-ASH1L Histone methyltransferase complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 13 Mar 2019.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,539
Mol. weight: 101.01 kDa
Ligands: SAM, ZN
Released: 13 Mar 2019

Explore 6AGO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AGO contains 43 α-helices and 40 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2049-2056	8
β-strand	2070-2071	2	1
β-strand	2076-2077	2	2
β-strand	2083	1	3
α-helix	2093-2096	4
α-helix	2102	1
β-strand	2103	1	4
α-helix	2109-2112	4
β-strand	2115	1	3
α-helix	2116-2118	3
α-helix	2125-2127	3
β-strand	2128	1	4
β-strand	2142-2146	5	5
β-strand	2152-2156	5	5
β-strand	2160	1	6
β-strand	2165-2168	4	3
β-strand	2172-2174	3	2
α-helix	2176-2185	10
α-helix	2190-2192	3
β-strand	2195-2197	3	2
β-strand	2203-2205	3	2
β-strand	2209-2210	2	1
α-helix	2212-2215	4
β-strand	2217-2218	2	7
β-strand	2224-2231	8	3
β-strand	2234-2241	8	3
β-strand	2245	1	6
α-helix	2249	1
β-strand	2250	1	5
α-helix	2251	1
β-strand	2252-2253	2	7

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2040-2042	3
α-helix	2049-2057	9
β-strand	2070-2071	2	8
β-strand	2076-2077	2	9
β-strand	2083	1	10
α-helix	2102	1
α-helix	2109-2112	4
β-strand	2115	1	10
α-helix	2116-2118	3
β-strand	2142-2146	5	11
β-strand	2152-2156	5	11
β-strand	2160	1	12
β-strand	2165-2168	4	10
β-strand	2172-2175	4	9
α-helix	2176-2184	9
β-strand	2195-2197	3	9
β-strand	2202-2205	4	9
β-strand	2209-2210	2	8
α-helix	2212-2215	4
β-strand	2224-2231	8	10
β-strand	2234-2241	8	10
β-strand	2245	1	12
β-strand	2250	1	11

Chain C: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	165-172	8
α-helix	173-177	5
β-strand	180-182	3	13
α-helix	186	1
α-helix	190-202	13
α-helix	211-232	22
α-helix	239-248	10
α-helix	254-256	3
α-helix	260-266	7
α-helix	270-274	5
α-helix	284-300	17
α-helix	302-305	4
α-helix	308-310	3
β-strand	311-313	3	13
α-helix	314-315	2

Chain D: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	159-161	3
α-helix	165-172	8
α-helix	173-177	5
β-strand	180-182	3	14
α-helix	190-200	11
α-helix	214-232	19
α-helix	239-248	10
α-helix	254-256	3
α-helix	260-267	8
α-helix	270-276	7
α-helix	284-300	17
α-helix	308-310	3
β-strand	311-313	3	14
α-helix	314-315	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase ASH1L	A, B	protein	256	Homo sapiens	Q9NR48
Mortality factor 4 like 1	C, D	protein	173	Homo sapiens	Q9UBU8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6AGO_1 Histone-lysine N-methyltransferase ASH1L (chains A, B)
GSGKYLRQKRIDFQLPYDILWQWKHNQLYKKPDVPLYKKIRSNVYVDVKPLSGYEATTCN
CKKPDDDTRKGCVDDCLNRMIFAECSPNTCPCGEQCCNQRIQRHEWVQCLERFRAEEKGW
GIRTKEPLKAGQFIIEYLGEVVSEQEFRNRMIEQYHNHSDHYCLNLDSGMVIDSYRMGNE
ARFINHSCDPNCEMQKWSVNGVYRIGLYALKDMPAGTELTYDYNFHSFNVEKQQLCKCGF
EKCRGIIGGKSQRVNG

Sequence of entity 2 (C, D), FASTA

>6AGO_2 Mortality factor 4 like 1 (chains C, D)
MNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK
EYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRI
GAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAE

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	6

Primary citation

Structural Basis of MRG15-Mediated Activation of the ASH1L Histone Methyltransferase by Releasing an Autoinhibitory Loop. Lee, Y., Yoon, E., Cho, S. et al. Structure (2019) 27:846. DOI 10.1016/j.str.2019.01.016 · PubMed

Other PDB entries of the same protein (UniProt Q9NR48), best resolution first:

8VLF 1.34 Å, Crystal structure of Ash1L PHD finger in complex with histone H3K4me3
6WZW 1.69 Å, Ash1L SET domain in complex with AS-85
6X0P 1.69 Å, Ash1L SET domain Q2265A mutant in complex with AS-5
8VLD 1.92 Å, Crystal structure of Ash1L PHD finger in complex with histone H3K4me2
4YNM 2.19 Å, ASH1L wild-type SET domain in complex with S-adenosyl methionine (SAM)
4YPE 2.2 Å, ASH1L SET domain H2193F mutant in complex with S-adenosyl methionine (SAM)
4YPA 2.3 Å, ASH1L SET domain Q2265A mutant in complex with S-adenosyl methionine (SAM)
8VLH 2.4 Å, Crystal structure of Ash1L PHD-BAH domains
3MQM 2.54 Å, Crystal Structure of the Bromodomain of human ASH1L
4YPU 2.6 Å, ASH1L SET domain K2264L mutant in complex with S-adenosyl methionine (SAM)
6INE 2.6 Å, Crystal Structure of human ASH1L-MRG15 complex
3OPE 2.9 Å, Structural Basis of Auto-inhibitory mechanism of Histone methyltransferase

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