SAXSdb — 2rfi

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

Histone-lysine N-methyltransferase, H3 lysine-9 specific 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 2	Histone H3 × 1 ZINC ION × 4 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone H3 × 1 ZINC ION × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Histone H3 × 2 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EHMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–285； UniProt 951–1235 Author chain B； PDBConstruct 1–285； UniProt 951–1235

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	2rfi
Deposition date deposition_date	2007-09-30
Structure title title	Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide
Keywords keywords	;EUCHROMATIC HISTONE METHYLTRANSFERASE 1, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, Alternative splicing, ANK repeat, Chromatin regulator, Nucleus, Phosphorylation, Polymorphism, S-adenosyl-L-methionine, Acetylation, Chromosomal protein, DNA damage, DNA repair, 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.

2rfi__assembly_2__model_1

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

Download this curve (.dat)

2rfi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rfi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.74 Å
Rg (electron density)	18.51 Å
Total Rg	19.56 Å
Atom count	2086
Residues	257
Excluded volume	36762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rfi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rfi__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2rfi__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
Molecular weight formula_weight	32830.2 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5068

NSQVWSALQMSKALQDSAPDRPSPVERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H3
Molecular weight formula_weight	1164.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

TKQTARKSTGG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	686

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2rfiA00
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	2rfiB00
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	84.593 Å
Unit-cell length b length_b	85.627 Å
Unit-cell length c length_c	95.670 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.590 Å
Low-resolution limit resolution_low	42.800 Å
R factor r_factor	0.1940
R_work r_work	0.1926
R_free r_free	0.2201

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide

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

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5

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

2rfi__assembly_2__model_1

2rfi__assembly_2__model_1 | I(q)

2rfi__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide

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

Histone-lysine N-methyltransferase, H3 lysine-9 specific 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2rfi__assembly_2__model_1

2rfi__assembly_2__model_1 | I(q)

2rfi__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)