4IKP: Histone-arginine methyltransferase CARM1

Name: PDB 4IKP: Crystal structure of coactivator-associated arginine methyltransferase 1 with methylenesinefungin
Published: 2013-02-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of coactivator-associated arginine methyltransferase 1 with methylenesinefungin. Determined by X-ray diffraction at 2.0 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,705
Mol. weight: 157.03 kDa
Ligands: 4IK
Released: 13 Feb 2013

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

Secondary structure: helices and β-sheets

4IKP contains 61 α-helices and 88 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: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	145-152	8
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	364-368	5
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 B: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	145-153	9
α-helix	156-163	8
α-helix	166-178	13
α-helix	180-182	3
β-strand	187-191	5	6
α-helix	197-204	8
β-strand	209-214	6	6
α-helix	218-228	11
β-strand	235-239	5	6
β-strand	251-256	6	6
β-strand	260	1	7
β-strand	263	1	7
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	6
β-strand	289-297	9	8
α-helix	300-310	11
α-helix	311-313	3
β-strand	318	1	9
β-strand	321	1	9
α-helix	324-326	3
α-helix	327-335	9
α-helix	338	1
β-strand	339-341	3	8
α-helix	345-347	3
β-strand	348	1	8
β-strand	353-358	6	8
α-helix	364-367	4
β-strand	369-377	9	10
β-strand	382-396	15	8
β-strand	401-405	5	8
β-strand	417-428	12	8
β-strand	433-443	11	10
β-strand	447-456	10	10
β-strand	462-468	7	10
β-strand	473-474	2	8

Chain C: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	144-152	9
α-helix	156-163	8
α-helix	166-178	13
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	311-314	4
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
β-strand	350	1	15
α-helix	351-352	2
β-strand	353-358	6	13
α-helix	364-367	4
β-strand	369-377	9	16
β-strand	378	1	15
β-strand	382-396	15	13
β-strand	401-405	5	13
α-helix	411-412	2
β-strand	417-428	12	13
β-strand	433-442	10	16
β-strand	448-456	9	16
β-strand	461-468	8	16
β-strand	473-474	2	13

Chain D: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	144-153	10
α-helix	156-163	8
α-helix	166-178	13
α-helix	180-182	3
β-strand	187-191	5	17
α-helix	197-204	8
β-strand	209-214	6	17
α-helix	218-228	11
β-strand	235-239	5	17
α-helix	246-247	2
β-strand	251-256	6	17
β-strand	260	1	18
β-strand	263	1	18
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	17
β-strand	289-297	9	19
α-helix	300-310	11
β-strand	318	1	20
β-strand	321	1	20
α-helix	324-326	3
α-helix	327-335	9
α-helix	338	1
β-strand	339-341	3	19
α-helix	345-347	3
β-strand	348	1	19
β-strand	350	1	21
β-strand	353-358	6	19
α-helix	364-367	4
β-strand	369-377	9	22
β-strand	378	1	21
β-strand	382-396	15	19
β-strand	401-405	5	19
β-strand	417-428	12	19
β-strand	433-443	11	22
β-strand	447-456	10	22
β-strand	462-468	7	22
β-strand	473-474	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-arginine methyltransferase CARM1	A, B, C, D	protein	341	Homo sapiens	Q86X55 (AlphaFold model)

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

>4IKP_1 Histone-arginine methyltransferase CARM1 (chains A, B, C, D)
RTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILS
FFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPM
GYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFH
GVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHML
HSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCL
LIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTT

Ligands and cofactors

ID	Name	Formula	Copies
4IK	(2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyte…	C16 H25 N7 O5	4

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

Primary citation

A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion. Cai, X.C., Zhang, T., Kim, E.J. et al. Elife (2019) 8. DOI 10.7554/eLife.47110 · 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
6ARV 2.0 Å, Crystal structure of CARM1 with Compound 2 and SAH

Browse structure collections

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