SAXSdb — 3f9z

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

Histone-lysine N-methyltransferase SETD8

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Histone H4 × 1 （P62805） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone H4 × 1 （P62805） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone H4 × 1 （P62805） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone H4 × 1 （P62805） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SETD8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–166； UniProt 232–393 Author chain B； PDBConstruct 5–166； UniProt 232–393 Author chain C； PDBConstruct 5–166； UniProt 232–393 Author chain D； PDBConstruct 5–166； UniProt 232–393

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 2	Histone-lysine N-methyltransferase SETD8 × 1 （Q9NQR1） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase SETD8 × 1 （Q9NQR1） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase SETD8 × 1 （Q9NQR1） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase SETD8 × 1 （Q9NQR1） S-ADENOSYL-L-HOMOCYSTEINE × 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	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–10； UniProt 16–25 Author chain F； PDBConstruct 1–10； UniProt 16–25 Author chain G； PDBConstruct 1–10； UniProt 16–25 Author chain H； PDBConstruct 1–10； UniProt 16–25

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	3f9z
Deposition date deposition_date	2008-11-14
Structure title title	Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy
Keywords keywords	;methyltransferase, histone, SET, lysine, Alternative splicing, Cell cycle, Cell division, Chromatin regulator, Chromosomal protein, Coiled coil, Mitosis, Nucleus, Repressor, S-adenosyl-L-methionine, Transcription, Transcription regulation, Acetylation, DNA-binding, Methylation, Nucleosome core, 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.

3f9z__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3f9z__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f9z__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.43 Å
Rg (electron density)	16.41 Å
Total Rg	17.54 Å
Atom count	1390
Residues	170
Excluded volume	24492 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f9z__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3f9z__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3f9z__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3f9z__assembly_4__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase SETD8
Molecular weight formula_weight	18774.3 kDa
EC 编号 ec_number	2.1.1.43
Mutation mutation	Y245F
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6115

GAMGSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEFHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	1284.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

AKRHRKVLRD

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	589

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3f9zA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	3f9zB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	3f9zC00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	3f9zD00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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Unit-cell length a length_a	43.990 Å
Unit-cell length b length_b	45.550 Å
Unit-cell length c length_c	94.410 Å
Unit-cell angle α angle_alpha	89.37 °
Unit-cell angle β angle_beta	87.09 °
Unit-cell angle γ angle_gamma	90.50 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	38.900 Å
R factor r_factor	0.2178
R_work r_work	0.2157
R_free r_free	0.2570

Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy

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

Histone-lysine N-methyltransferase SETD8

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

3f9z__assembly_2__model_1

3f9z__assembly_2__model_1 | I(q)

3f9z__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy

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

Histone-lysine N-methyltransferase SETD8

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

3f9z__assembly_2__model_1

3f9z__assembly_2__model_1 | I(q)

3f9z__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)