2Y1W: Histone-arginine methyltransferase CARM1

Name: PDB 2Y1W: Crystal structure of coactivator associated arginine methyltransferase 1 (CARM1) in complex with sinefungin and indole inhibitor
Published: 2011-03-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of coactivator associated arginine methyltransferase 1 (CARM1) in complex with sinefungin and indole inhibitor. Determined by X-ray diffraction at 2.1 Å resolution. Released 23 Mar 2011.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 11,580
Mol. weight: 160.97 kDa
Ligands: 849, SFG
Released: 23 Mar 2011

Explore 2Y1W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Y1W contains 68 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: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	137-141	5
α-helix	144-154	11
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	312-314	3
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
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: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	137-141	5
α-helix	144-154	11
α-helix	157-164	8
α-helix	167-179	13
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
α-helix	312-315	4
β-strand	319	1	10
β-strand	322	1	10
α-helix	325-327	3
α-helix	328-336	9
α-helix	339	1
β-strand	340-342	3	9
α-helix	346-348	3
β-strand	349	1	9
α-helix	352-353	2
β-strand	354-359	6	9
α-helix	365-368	4
β-strand	370-378	9	11
β-strand	383-397	15	9
β-strand	402-406	5	9
β-strand	418-429	12	9
β-strand	434-443	10	11
β-strand	449-457	9	11
β-strand	462-469	8	11
β-strand	474-475	2	9

Chain C: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	137-141	5
α-helix	144-153	10
α-helix	157-164	8
α-helix	167-179	13
α-helix	181-183	3
β-strand	188-192	5	12
α-helix	198-205	8
β-strand	210-215	6	12
α-helix	219-229	11
β-strand	236-240	5	12
β-strand	252-257	6	12
β-strand	261	1	13
β-strand	264	1	13
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	12
β-strand	290-298	9	14
α-helix	301-311	11
α-helix	312-315	4
β-strand	319	1	15
β-strand	322	1	15
α-helix	325-327	3
α-helix	328-337	10
β-strand	340-342	3	14
α-helix	346-348	3
β-strand	349	1	14
α-helix	352-353	2
β-strand	354-359	6	14
α-helix	365-368	4
β-strand	370-378	9	16
β-strand	383-397	15	14
β-strand	402-406	5	14
β-strand	418-429	12	14
β-strand	434-443	10	16
β-strand	449-457	9	16
β-strand	462-469	8	16
β-strand	474-475	2	14

Chain D: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	137-141	5
α-helix	144-154	11
α-helix	157-164	8
α-helix	167-178	12
α-helix	181-183	3
β-strand	188-192	5	17
α-helix	198-205	8
β-strand	210-215	6	17
α-helix	219-229	11
β-strand	236-240	5	17
β-strand	252-257	6	17
β-strand	261	1	18
β-strand	264	1	18
α-helix	266-268	3
α-helix	269-275	7
α-helix	276-279	4
β-strand	280-287	8	17
β-strand	290-298	9	19
α-helix	301-311	11
α-helix	312-314	3
β-strand	319	1	20
β-strand	322	1	20
α-helix	325-327	3
α-helix	328-336	9
α-helix	339	1
β-strand	340-342	3	19
α-helix	346-348	3
β-strand	349	1	19
α-helix	352-353	2
β-strand	354-359	6	19
α-helix	365-368	4
β-strand	370-378	9	21
β-strand	383-397	15	19
β-strand	402-406	5	19
β-strand	418-429	12	19
β-strand	434-443	10	21
β-strand	449-457	9	21
β-strand	463-469	7	21
β-strand	474-475	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-arginine methyltransferase CARM1	A, B, C, D	protein	348	HOMO SAPIENS	Q86X55 (AlphaFold model)

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

>2Y1W_1 HISTONE-ARGININE METHYLTRANSFERASE CARM1 (chains A, B, C, D)
SVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCG
SGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDII
ISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWY
QPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPF
KFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTL
SGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPS

Ligands and cofactors

ID	Name	Formula	Copies
849	2-{4-[3-fluoro-2-(2-methoxyphenyl)-1H-indol-5-yl]…	C23 H28 F N3 O	4
SFG	Sinefungin	C15 H23 N7 O5	4

Primary citation

Structural Basis for Carm1 Inhibition by Indole and Pyrazole Inhibitors. Sack, J.S., Thieffine, S., Bandiera, T. et al. Biochem J (2011) 436:331. DOI 10.1042/BJ20102161 · 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…

Browse structure collections

About this viewer

MolViewer shows 2Y1W directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.