5U4X: Histone-arginine methyltransferase CARM1

Name: PDB 5U4X: Coactivator-associated arginine methyltransferase 1 with TP-064
Published: 2016-12-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Coactivator-associated arginine methyltransferase 1 with TP-064. Determined by X-ray diffraction at 1.88 Å resolution. Released 21 Dec 2016.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,750
Mol. weight: 158.36 kDa
Ligands: SAH, 7VM
Released: 21 Dec 2016

Explore 5U4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U4X contains 63 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.

Chain A: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	148-154	7
α-helix	157-164	8
α-helix	167-179	13
α-helix	181-183	3
β-strand	188-192	5	1
α-helix	198-205	8
β-strand	210-215	6	1
α-helix	219-229	11
β-strand	236-240	5	1
β-strand	252-257	6	1
β-strand	261	1	2
β-strand	264	1	2
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	1
β-strand	290-298	9	3
α-helix	301-311	11
α-helix	312-315	4
β-strand	319	1	4
β-strand	322	1	4
α-helix	325-327	3
α-helix	328-336	9
α-helix	339	1
β-strand	340-342	3	3
α-helix	346-348	3
β-strand	349	1	3
α-helix	352-353	2
β-strand	354-359	6	3
α-helix	365-369	5
β-strand	370-378	9	5
β-strand	383-397	15	3
β-strand	402-406	5	3
β-strand	418-429	12	3
β-strand	434-443	10	5
β-strand	449-457	9	5
β-strand	462-469	8	5
β-strand	474-475	2	3

Chain B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	148-154	7
α-helix	157-164	8
α-helix	167-179	13
α-helix	181-183	3
β-strand	188-192	5	6
α-helix	198-205	8
β-strand	210-215	6	6
α-helix	219-229	11
β-strand	236-240	5	6
β-strand	252-257	6	6
β-strand	261	1	7
β-strand	264	1	7
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	6
β-strand	290-298	9	8
α-helix	301-311	11
α-helix	312-314	3
β-strand	319	1	9
β-strand	322	1	9
α-helix	325-327	3
α-helix	328-336	9
α-helix	339	1
β-strand	340-342	3	8
α-helix	346-348	3
β-strand	349	1	8
α-helix	352-353	2
β-strand	354-359	6	8
α-helix	365-368	4
β-strand	370-378	9	10
β-strand	383-397	15	8
β-strand	402-406	5	8
β-strand	418-429	12	8
β-strand	434-443	10	10
β-strand	449-457	9	10
β-strand	463-469	7	10
β-strand	474-475	2	8

Chain C: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	148-154	7
α-helix	157-164	8
α-helix	167-179	13
α-helix	181-183	3
β-strand	188-192	5	11
α-helix	198-205	8
β-strand	210-215	6	11
α-helix	219-229	11
β-strand	236-240	5	11
β-strand	252-257	6	11
β-strand	261	1	12
β-strand	264	1	12
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	11
β-strand	290-298	9	13
α-helix	301-311	11
α-helix	312-315	4
β-strand	319	1	14
β-strand	322	1	14
α-helix	325-327	3
α-helix	328-336	9
α-helix	339	1
β-strand	340-342	3	13
α-helix	346-348	3
β-strand	349	1	13
α-helix	352-353	2
β-strand	354-359	6	13
α-helix	365-368	4
β-strand	370-378	9	15
β-strand	383-397	15	13
β-strand	402-406	5	13
β-strand	418-429	12	13
β-strand	434-443	10	15
β-strand	449-457	9	15
β-strand	462-469	8	15
β-strand	474-475	2	13

Chain D: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	148-154	7
α-helix	157-164	8
α-helix	167-179	13
α-helix	181-183	3
β-strand	188-192	5	16
α-helix	198-205	8
β-strand	210-215	6	16
α-helix	219-229	11
β-strand	236-240	5	16
β-strand	252-257	6	16
β-strand	261	1	17
β-strand	264	1	17
α-helix	270-275	6
α-helix	276-279	4
β-strand	280-287	8	16
β-strand	290-298	9	18
α-helix	301-311	11
α-helix	312-314	3
β-strand	319	1	19
β-strand	322	1	19
α-helix	325-327	3
α-helix	328-336	9
α-helix	339	1
β-strand	340-342	3	18
α-helix	346-348	3
β-strand	349	1	18
β-strand	351	1	20
β-strand	354-359	6	18
α-helix	365-368	4
β-strand	370-378	9	21
β-strand	379	1	20
β-strand	383-397	15	18
β-strand	402-406	5	18
β-strand	418-429	12	18
β-strand	434-443	10	21
β-strand	449-457	9	21
β-strand	463-469	7	21
β-strand	474-475	2	18

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

>5U4X_1 Histone-arginine methyltransferase CARM1 (chains A, B, C, D)
RTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILS
FFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPM
GYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFH
GVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHML
HSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCL
LIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTT

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	4
7VM	N-methyl-N-[(2-{1-[2-(methylamino)ethyl]piperidin-4-yl}pyridin-4-yl)methyl]-3-p…	C28 H34 N4 O2	4

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

Primary citation

TP-064, a potent and selective small molecule inhibitor of PRMT4 for multiple myeloma. Nakayama, K., Szewczyk, M.M., Dela Sena, C. et al. Oncotarget (2018) 9:18480-18493. DOI 10.18632/oncotarget.24883 · 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
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…
6ARV 2.0 Å, Crystal structure of CARM1 with Compound 2 and SAH

Browse structure collections

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