5LV3: Mouse CARM1

Name: PDB 5LV3: Crystal structure of mouse CARM1 in complex with ligand LH1561Br
Published: 2017-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of mouse CARM1 in complex with ligand LH1561Br. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Mus musculus
Chains: 4
Atoms: 12,241
Mol. weight: 165.38 kDa
Ligands: SAH, LHF
Released: 20 Sept 2017

Explore 5LV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LV3 contains 64 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: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	137-141	5
α-helix	144-154	11
α-helix	157-165	9
α-helix	167-178	12
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
α-helix	352-353	2
β-strand	354-359	6	3
α-helix	365-368	4
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	434-444	11	5
β-strand	448-457	10	5
β-strand	463-469	7	5
β-strand	474-475	2	3

Chain B: 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	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	312-315	4
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
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	434-444	11	10
β-strand	448-457	10	10
β-strand	462-469	8	10
β-strand	474-475	2	8

Chain C: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	137-141	5
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	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	312-314	3
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
β-strand	351	1	15
β-strand	354-359	6	13
α-helix	365-368	4
β-strand	370-378	9	16
β-strand	379	1	15
β-strand	383-397	15	13
β-strand	402-406	5	13
β-strand	418-429	12	13
β-strand	434-444	11	16
β-strand	448-457	10	16
β-strand	463-469	7	16
β-strand	474-475	2	13

Chain D: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	137-140	4
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	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	269-275	7
α-helix	276-279	4
β-strand	280-287	8	17
β-strand	290-298	9	19
α-helix	301-312	12
α-helix	313-315	3
β-strand	319	1	20
β-strand	322	1	20
α-helix	325-327	3
α-helix	328-336	9
β-strand	340-342	3	19
α-helix	346-348	3
β-strand	349	1	19
β-strand	351	1	21
α-helix	352-353	2
β-strand	354-359	6	19
β-strand	370-378	9	22
β-strand	379	1	21
β-strand	383-397	15	19
β-strand	402-406	5	19
β-strand	418-429	12	19
β-strand	434-443	10	22
β-strand	449-457	9	22
β-strand	462-469	8	22
β-strand	474-475	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-arginine methyltransferase CARM1	A, B, C, D	protein	361	Mus musculus	Q9WVG6 (AlphaFold model)

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

>5LV3_1 Histone-arginine methyltransferase CARM1 (chains A, B, C, D)
GHMGHTLERSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKD
KIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEV
SLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYME
QFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEG
DLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSP
LFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPP
G

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2
LHF	5-[[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-…	C24 H28 Br N9 O5	2

Primary citation

Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Halby, L., Marechal, N., Pechalrieu, D. et al. Philos Trans R Soc Lond B Biol Sci (2018) 373. DOI 10.1098/rstb.2017.0072 · PubMed

Other PDB entries of the same protein (UniProt Q9WVG6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IH3 1.77 Å, Crystal structure of mouse CARM1 in complex with SAH at 1.8 Angstroms resolution
7QPH 1.9 Å, Crystal structure of mouse CARM1 in complex with histone H3_22-31 K27 acetylated
5K8X 1.99 Å, Crystal structure of mouse CARM1 in complex with inhibitor U3
5ISB 2.0 Å, Crystal structure of mouse CARM1 in complex with inhibitor SA0435
5LGR 2.0 Å, Crystal structure of mouse CARM1 in complex with ligand P1C3u
7QRD 2.0 Å, Crystal structure of mouse CARM1 in complex with histone H3_10-25
5IS6 2.01 Å, Crystal structure of mouse CARM1 in complex with Sinefungin at 2.0 Angstroms resolution
5LGP 2.04 Å, Crystal structure of mouse CARM1 in complex with ligand P1C3s
7PUQ 2.09 Å, CARM1 in complex with EML982
5ISE 2.1 Å, Crystal structure of mouse CARM1 in complex with inhibitor SA0649
5K8W 2.1 Å, Crystal structure of mouse CARM1 in complex with inhibitor U2
5LGS 2.1 Å, Crystal structure of mouse CARM1 in complex with ligand P2C3u

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