5DX1: CARM1, sinefungin, and PABP1 peptide

Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455). Determined by X-ray diffraction at 1.93 Å resolution. Released 25 Nov 2015.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,231
Mol. weight: 168.08 kDa
Ligands: SFG
Released: 25 Nov 2015

Explore 5DX1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DX1 contains 68 α-helices and 86 β-strands across 8 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	136-140	5
α-helix	143-153	11
α-helix	156-164	9
α-helix	166-178	13
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
α-helix	338	1
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	364-367	4
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: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	136-140	5
α-helix	143-153	11
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	269-274	6
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
β-strand	339-341	3	8
α-helix	345-347	3
β-strand	348	1	8
α-helix	351-352	2
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, 21 β-strands

Element	Residues	Length	Sheet
α-helix	136-140	5
α-helix	143-153	11
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
α-helix	351-352	2
β-strand	353-358	6	13
α-helix	364-367	4
β-strand	369-377	9	15
β-strand	382-396	15	13
β-strand	401-405	5	13
β-strand	417-428	12	13
β-strand	433-442	10	15
β-strand	448-456	9	15
β-strand	461-468	8	15
β-strand	473-474	2	13

Chain D: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	136-140	5
α-helix	143-153	11
α-helix	156-163	8
α-helix	166-178	13
α-helix	180-182	3
β-strand	187-191	5	16
α-helix	197-204	8
β-strand	209-214	6	16
α-helix	218-228	11
β-strand	235-239	5	16
β-strand	251-256	6	16
β-strand	260	1	17
β-strand	263	1	17
α-helix	268-274	7
α-helix	275-278	4
β-strand	279-286	8	16
β-strand	289-297	9	18
α-helix	300-310	11
α-helix	311-313	3
β-strand	318	1	19
β-strand	321	1	19
α-helix	324-326	3
α-helix	327-335	9
β-strand	339-341	3	18
α-helix	345-347	3
β-strand	348	1	18
β-strand	350	1	20
β-strand	353-358	6	18
α-helix	364-367	4
β-strand	369-377	9	21
β-strand	378	1	20
β-strand	382-396	15	18
β-strand	401-405	5	18
β-strand	417-428	12	18
β-strand	433-442	10	21
β-strand	448-456	9	21
β-strand	461-468	8	21
β-strand	473-474	2	18

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-arginine methyltransferase CARM1	A, B, C, D	protein	349	Homo sapiens	Q86X55 (AlphaFold model)
PABP1 peptide	F, G, H, I	protein	19	Homo sapiens	P11940 (AlphaFold model)

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

>5DX1_1 Histone-arginine methyltransferase CARM1 (chains A, B, C, D)
SIARSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLD
VGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQ
VDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKA
NFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRI
EIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKA
GDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGT

Sequence of entity 2 (F, G, H, I), FASTA

>5DX1_2 PABP1 peptide (chains F, G, H, I)
NMPGAIRPAAPRPPFSTMX

Ligands and cofactors

ID	Name	Formula	Copies
SFG	Sinefungin	C15 H23 N7 O5	4

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

Primary citation

Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates. Boriack-Sjodin, P.A., Jin, L., Jacques, S.L. et al. ACS Chem Biol (2016) 11:763-771. DOI 10.1021/acschembio.5b00773 · 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
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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