5lv2

Crystal structure of mouse CARM1 in complex with inhibitor LH1246

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-arginine methyltransferase CARM1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 1,2-ETHANEDIOL × 5 ;5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one ; × 2 TETRAETHYLENE GLYCOL × 2 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE × 1 1,2-DIMETHOXYETHANE × 1 DI(HYDROXYETHYL)ETHER × 1 SODIUM ION × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 1,2-ETHANEDIOL × 8 ;5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one ; × 2 TETRAETHYLENE GLYCOL × 2 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE × 1 SODIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CARM1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–361； UniProt 130–487 Author chain B； PDBConstruct 4–361； UniProt 130–487 Author chain C； PDBConstruct 4–361； UniProt 130–487 Author chain D； PDBConstruct 4–361； UniProt 130–487 Author chain E； PDBConstruct 4–361； UniProt 130–487 Author chain F； PDBConstruct 4–361； UniProt 130–487 Author chain G； PDBConstruct 4–361； UniProt 130–487 Author chain H； PDBConstruct 4–361； UniProt 130–487

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lv2
Deposition date deposition_date	2016-09-12
Structure title title	Crystal structure of mouse CARM1 in complex with inhibitor LH1246
Keywords keywords	;PROTEIN ARGININE METHYLTRANSFERASE, CATALYTIC DOMAIN, CHROMATIN REGULATOR, MRNA PROCESSING, MRNA SPLICING, NUCLEUS, S-ADENOSYL-L-METHIONINE, TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5lv2__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5lv2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lv2__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.77 Å
Rg (electron density)	39.45 Å
Total Rg	39.89 Å
Atom count	22166
Residues	1371
Excluded volume	199950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lv2__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5lv2__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Histone-arginine methyltransferase CARM1
Molecular weight formula_weight	40850.5 kDa
EC 编号 ec_number	2.1.1.319
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	45590

GHMGHTLERSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPPG

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
Molecular weight formula_weight	385.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	;5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one ;
Molecular weight formula_weight	433.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	1-METHOXY-2-(2-METHOXYETHOXY)ETHANE
Molecular weight formula_weight	134.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	1,2-DIMETHOXYETHANE
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1166

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	5lv2A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2A02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2B02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2C02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2D02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2E02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2F02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2G01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2G02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

Domain ID domain_id	5lv2H01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5lv2H02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	160 — Hnrnp arginine n-methyltransferase1
Homologous superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

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Unit-cell length a length_a	98.684 Å
Unit-cell length b length_b	74.832 Å
Unit-cell length c length_c	206.639 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	49.340 Å
R factor r_factor	0.2067
R_work r_work	0.2051
R_free r_free	0.2380

Crystal structure of mouse CARM1 in complex with inhibitor LH1246

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-arginine methyltransferase CARM1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5lv2__assembly_1__model_1

5lv2__assembly_1__model_1 | I(q)

5lv2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of mouse CARM1 in complex with inhibitor LH1246

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-arginine methyltransferase CARM1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5lv2__assembly_1__model_1

5lv2__assembly_1__model_1 | I(q)

5lv2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)