6S79: CARM1

Name: PDB 6S79: Crystal structure of CARM1 in complex with inhibitor AA183
Published: 2020-03-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of CARM1 in complex with inhibitor AA183. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,521
Mol. weight: 162.28 kDa
Ligands: KXW
Released: 4 Mar 2020

Explore 6S79 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S79 contains 64 α-helices and 86 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.

Chains A and B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	136-140	5
α-helix	143-153	11
α-helix	156-163	8
α-helix	166-177	12
α-helix	180-182	3
β-strand	187-191	5	1
α-helix	197-204	8
β-strand	209-214	6	1
α-helix	218-228	11
β-strand	235-239	5	1
β-strand	251-256	6	1
β-strand	260	1	2
β-strand	263	1	2
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	1
β-strand	289-297	9	3
α-helix	300-310	11
α-helix	311-314	4
β-strand	318	1	4
β-strand	321	1	4
α-helix	324-326	3
α-helix	327-335	9
β-strand	339-341	3	3
α-helix	345-347	3
β-strand	348	1	3
α-helix	351-352	2
β-strand	353-358	6	3
α-helix	364-367	4
β-strand	369-377	9	5
β-strand	382-396	15	3
β-strand	401-405	5	3
β-strand	417-428	12	3
β-strand	433-442	10	5
β-strand	448-456	9	5
β-strand	461-468	8	5
β-strand	473-474	2	3

Chain C: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	136-140	5
α-helix	143-153	11
α-helix	156-163	8
α-helix	166-177	12
α-helix	180-182	3
β-strand	187-191	5	11
α-helix	197-204	8
β-strand	209-214	6	11
α-helix	218-228	11
β-strand	235-239	5	11
β-strand	251-256	6	11
β-strand	260	1	12
β-strand	263	1	12
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	11
β-strand	289-297	9	13
α-helix	300-310	11
α-helix	311-313	3
β-strand	318	1	14
β-strand	321	1	14
α-helix	324-326	3
α-helix	327-335	9
β-strand	339-341	3	13
α-helix	345-347	3
β-strand	348	1	13
α-helix	351-352	2
β-strand	353-358	6	13
α-helix	364-367	4
β-strand	369-377	9	15
β-strand	382-396	15	13
β-strand	401-405	5	13
β-strand	417-428	12	13
β-strand	433-443	11	15
β-strand	447-456	10	15
β-strand	462-468	7	15
β-strand	473-474	2	13

Chain D: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	136-140	5
α-helix	143-153	11
α-helix	156-163	8
α-helix	166-177	12
α-helix	180-182	3
β-strand	187-191	5	16
α-helix	197-204	8
β-strand	209-214	6	16
α-helix	218-228	11
β-strand	235-239	5	16
β-strand	251-256	6	16
β-strand	260	1	17
β-strand	263	1	17
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	16
β-strand	289-297	9	18
α-helix	300-310	11
α-helix	311-313	3
β-strand	318	1	19
β-strand	321	1	19
α-helix	324-326	3
α-helix	327-335	9
β-strand	339-341	3	18
α-helix	345-347	3
β-strand	348	1	18
β-strand	350	1	20
α-helix	351-352	2
β-strand	353-358	6	18
α-helix	364-367	4
β-strand	369-377	9	21
β-strand	378	1	20
β-strand	382-396	15	18
β-strand	401-405	5	18
β-strand	417-428	12	18
β-strand	433-442	10	21
β-strand	448-456	9	21
β-strand	462-468	7	21
β-strand	473-474	2	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-arginine methyltransferase CARM1	A, B, C, D	protein	351	Homo sapiens	Q86X55 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6S79_1 Histone-arginine methyltransferase CARM1 (chains A, B, C, D)
SVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCG
SGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDII
ISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWY
QPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPF
KFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTL
SGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
KXW	(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)ox…	C22 H31 N9 O5	4

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural and biochemical evaluation of bisubstrate inhibitors of protein arginine N-methyltransferases PRMT1 and CARM1 (PRMT4). Gunnell, E.A., Al-Noori, A., Muhsen, U. et al. Biochem J (2020) 477:787-800. DOI 10.1042/BCJ20190826 · PubMed

Other PDB entries of the same protein (UniProt Q86X55 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G2H 1.49 Å, Crystal Structure of PRMT4 with Compound YD1113
6DVR 1.54 Å, Crystal structure of human CARM1 with (R)-SKI-72
8SIG 1.78 Å, Crystal Structure of PRMT4 with Compound YD1-288
6S7A 1.86 Å, Crystal structure of CARM1 in complex with inhibitor AA175
8UQH 1.87 Å, X-ray crystal structure of PRMT4 bound to compound YD-1130
5U4X 1.88 Å, Coactivator-associated arginine methyltransferase 1 with TP-064
6ARJ 1.92 Å, Crystal structure of CARM1 with EPZ022302 and SAH
5DX1 1.93 Å, Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455)
5DX8 1.94 Å, Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455)
5DXJ 1.95 Å, Crystal structure of CARM1 and sinefungin
9O6H 1.97 Å, The Structure of PRMT4 in complex with SGC8172
4IKP 2.0 Å, Crystal structure of coactivator-associated arginine methyltransferase 1 with…

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