9zl3

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18

Method: X-RAY DIFFRACTION

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

Protein arginine N-methyltransferase 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Methylosome protein 50 × 4 （Q9BQA1） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 N~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-{(1R)-1-[2-fluoro-4-(trifluoromethyl)phenyl]ethyl}-N~1~-methylethanediamide × 4 DI(HYDROXYETHYL)ETHER × 32 1,2-ETHANEDIOL × 136 CHLORIDE ION × 16 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ANM5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–645； UniProt 2–637

Methylosome protein 50

Homo sapiens

UniProt Q9BQA1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Protein arginine N-methyltransferase 5 × 4 （O14744） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 N~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-{(1R)-1-[2-fluoro-4-(trifluoromethyl)phenyl]ethyl}-N~1~-methylethanediamide × 4 DI(HYDROXYETHYL)ETHER × 32 1,2-ETHANEDIOL × 136 CHLORIDE ION × 16 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MEP50_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 10–350； UniProt 2–342

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	9zl3
Deposition date deposition_date	2025-12-08
Structure title title	Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18
Keywords keywords	methyltransferase, SAM, MTAP-null, MTA-cooperative, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
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.

9zl3__assembly_1__model_1

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

Download this curve (.dat)

9zl3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9zl3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.61 Å
Rg (electron density)	50.16 Å
Total Rg	50.28 Å
Atom count	30152
Residues	3680
Excluded volume	536170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9zl3__assembly_1__model_1`	octameric （8）	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 (8)

Entity 1 Entity 1 polymer

Description description	Protein arginine N-methyltransferase 5
Molecular weight formula_weight	73763.6 kDa
EC 编号 ec_number	2.1.1.320
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8122

MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Methylosome protein 50
Molecular weight formula_weight	37862.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHHHHHHHHRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	5'-DEOXY-5'-METHYLTHIOADENOSINE
Molecular weight formula_weight	297.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-{(1R)-1-[2-fluoro-4-(trifluoromethyl)phenyl]ethyl}-N~1~-methylethanediamide
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	34

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	487

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Unit-cell length a length_a	102.367 Å
Unit-cell length b length_b	138.128 Å
Unit-cell length c length_c	178.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	1.710 Å
Low-resolution limit resolution_low	33.620 Å
R factor r_factor	0.1914
R_work r_work	0.1889
R_free r_free	0.2390

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18

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

Protein arginine N-methyltransferase 5

State in the Current Structure

Other States of the Same Protein in the Database

Methylosome protein 50

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

9zl3__assembly_1__model_1

9zl3__assembly_1__model_1 | I(q)

9zl3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

7. Citations (1)

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18

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

Protein arginine N-methyltransferase 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methylosome protein 50

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

9zl3__assembly_1__model_1

9zl3__assembly_1__model_1 | I(q)

9zl3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

7. Citations (1)