8UQH: PRMT4

Name: PDB 8UQH: X-ray crystal structure of PRMT4 bound to compound YD-1130
Published: 2025-04-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

X-ray crystal structure of PRMT4 bound to compound YD-1130. Determined by X-ray diffraction at 1.87 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,191
Mol. weight: 157.08 kDa
Ligands: X9L
Released: 2 Apr 2025

Explore 8UQH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UQH contains 59 α-helices and 90 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, 23 β-strands

Element	Residues	Length	Sheet
α-helix	143-154	12
α-helix	157-164	8
α-helix	167-178	12
α-helix	181-183	3
β-strand	185	1	1
β-strand	188-192	5	2
α-helix	198-205	8
β-strand	208	1	1
β-strand	210-215	6	2
α-helix	219-229	11
β-strand	236-240	5	2
β-strand	252-257	6	2
α-helix	262-264	3
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	2
β-strand	290-298	9	3
α-helix	301-311	11
α-helix	312-314	3
β-strand	319	1	4
β-strand	322	1	4
α-helix	325-327	3
α-helix	328-336	9
β-strand	340-342	3	3
α-helix	346-348	3
β-strand	349	1	3
β-strand	351	1	5
α-helix	352-353	2
β-strand	354-359	6	3
α-helix	365-368	4
β-strand	370-378	9	6
β-strand	379	1	5
β-strand	383-397	15	3
β-strand	402-406	5	3
β-strand	418-429	12	3
β-strand	434-443	10	6
β-strand	449-457	9	6
β-strand	463-469	7	6
β-strand	474-475	2	3

Chain B: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	144-153	10
α-helix	157-164	8
α-helix	167-178	12
α-helix	181-183	3
β-strand	188-192	5	7
α-helix	198-205	8
β-strand	210-215	6	7
α-helix	219-229	11
β-strand	236-240	5	7
β-strand	252-257	6	7
β-strand	261	1	8
β-strand	264	1	8
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	7
β-strand	290-298	9	9
α-helix	301-311	11
β-strand	319	1	10
β-strand	322	1	10
α-helix	325-327	3
α-helix	328-336	9
β-strand	340-342	3	9
α-helix	346-348	3
β-strand	349	1	9
β-strand	351	1	11
β-strand	354-359	6	9
α-helix	365-368	4
β-strand	370-378	9	12
β-strand	379	1	11
β-strand	383-397	15	9
β-strand	402-406	5	9
β-strand	418-429	12	9
β-strand	434-443	10	12
β-strand	449-457	9	12
β-strand	463-469	7	12
β-strand	474-475	2	9

Chain C: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	143-154	12
α-helix	157-164	8
α-helix	167-179	13
α-helix	181-183	3
β-strand	188-192	5	13
α-helix	198-205	8
β-strand	210-215	6	13
α-helix	219-229	11
β-strand	236-240	5	13
β-strand	252-257	6	13
β-strand	261	1	14
β-strand	264	1	14
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	13
β-strand	290-298	9	15
α-helix	301-311	11
α-helix	312-315	4
β-strand	319	1	16
β-strand	322	1	16
α-helix	325-327	3
α-helix	328-336	9
β-strand	340-342	3	15
α-helix	346-348	3
β-strand	349	1	15
α-helix	352-353	2
β-strand	354-359	6	15
α-helix	365-369	5
β-strand	370-378	9	17
β-strand	383-397	15	15
β-strand	402-406	5	15
β-strand	418-429	12	15
β-strand	434-444	11	17
β-strand	448-457	10	17
β-strand	462-469	8	17
β-strand	474-475	2	15

Chain D: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	143-154	12
α-helix	157-164	8
α-helix	167-178	12
α-helix	181-183	3
β-strand	188-192	5	18
α-helix	198-205	8
β-strand	210-215	6	18
α-helix	219-229	11
β-strand	236-240	5	18
β-strand	252-257	6	18
β-strand	261	1	19
β-strand	264	1	19
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	18
β-strand	290-298	9	20
α-helix	301-312	12
α-helix	313-315	3
β-strand	319	1	21
β-strand	322	1	21
α-helix	325-327	3
α-helix	328-336	9
β-strand	340-342	3	20
α-helix	346-348	3
β-strand	349	1	20
β-strand	351	1	22
α-helix	352-353	2
β-strand	354-359	6	20
α-helix	365-368	4
β-strand	370-378	9	23
β-strand	379	1	22
β-strand	383-397	15	20
β-strand	402-406	5	20
β-strand	418-429	12	20
β-strand	434-444	11	23
β-strand	448-457	10	23
β-strand	462-469	8	23
β-strand	474-475	2	20

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

>8UQH_1 Histone-arginine methyltransferase CARM1 (chains A, B, C, D)
ERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGIL
SFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEP
MGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSF
HGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHM
LHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTC
LLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGT

Ligands and cofactors

ID	Name	Formula	Copies
X9L	5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine	C19 H23 Br N6 O3 S	4

Primary citation

An Adenosine Analogue Library Reveals Insights into Active Sites of Protein Arginine Methyltransferases and Enables the Discovery of a Selective PRMT4 Inhibitor. Deng, Y., Kim, E.J., Song, X. et al. J Med Chem (2024) 67:18053-18069. DOI 10.1021/acs.jmedchem.4c01041 · 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
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…
6ARV 2.0 Å, Crystal structure of CARM1 with Compound 2 and SAH

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