SAXSdb — 5fa5

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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 12	Methylosome protein 50 × 4 （Q9BQA1） Histone H4 × 4 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Methylosome protein 50 × 2 （Q9BQA1） Histone H4 × 2 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Methylosome protein 50 × 2 （Q9BQA1） Histone H4 × 2 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Methylosome protein 50 × 1 （Q9BQA1） Histone H4 × 1 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 water × 2	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 14–650； UniProt 1–637

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 12	Protein arginine N-methyltransferase 5 × 4 （O14744） Histone H4 × 4 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Protein arginine N-methyltransferase 5 × 2 （O14744） Histone H4 × 2 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Protein arginine N-methyltransferase 5 × 2 （O14744） Histone H4 × 2 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Protein arginine N-methyltransferase 5 × 1 （O14744） Histone H4 × 1 （P62805） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 water × 2	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 27–367； UniProt 2–342

Histone H4

OrganismNot specified

UniProt P62805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Protein arginine N-methyltransferase 5 × 4 （O14744） Methylosome protein 50 × 4 （Q9BQA1） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Protein arginine N-methyltransferase 5 × 2 （O14744） Methylosome protein 50 × 2 （Q9BQA1） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Protein arginine N-methyltransferase 5 × 2 （O14744） Methylosome protein 50 × 2 （Q9BQA1） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Protein arginine N-methyltransferase 5 × 1 （O14744） Methylosome protein 50 × 1 （Q9BQA1） 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 2–21

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	5fa5
Deposition date deposition_date	2015-12-10
Structure title title	Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide
Keywords keywords	Methyl Transferase, TRANSFERASE-PROTEIN BINDING complex; TRANSFERASE/PROTEIN BINDING
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.

5fa5__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5fa5__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fa5__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	45.17 Å
Rg (electron density)	44.98 Å
Total Rg	45.21 Å
Atom count	14746
Residues	1854
Excluded volume	261340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fa5__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5fa5__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5fa5__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5fa5__assembly_4__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Protein arginine N-methyltransferase 5
Molecular weight formula_weight	74281.2 kDa
EC 编号 ec_number	2.1.1.-,2.1.1.125
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	7541

MDYKDDDDKGRATMAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Methylosome protein 50
Molecular weight formula_weight	39857.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSYYHHHHHHDYDLPTTENLYFQGSLRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Histone H4
Molecular weight formula_weight	2001.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SGRGKGGKGLGKGGAKRHRK

Entity 4 Entity 4 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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5fa5A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	5fa5A02
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	5fa5A03
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	5fa5B00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	102.050 Å
Unit-cell length b length_b	137.850 Å
Unit-cell length c length_c	178.430 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	—

Resolution resolution	2.340 Å
Low-resolution limit resolution_low	89.220 Å
R factor r_factor	0.1792
R_work r_work	0.1770
R_free r_free	0.2213

Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide

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

Histone H4

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

5fa5__assembly_3__model_1

5fa5__assembly_3__model_1 | I(q)

5fa5__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide

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

Histone H4

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

5fa5__assembly_3__model_1

5fa5__assembly_3__model_1 | I(q)

5fa5__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)