SAXSdb — 8y77

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

Sterile alpha motif domain-containing protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Lethal(3)malignant brain tumor-like protein 3 × 2 （Q96JM7） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Lethal(3)malignant brain tumor-like protein 3 × 1 （Q96JM7） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAMD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–66； UniProt 459–523

Lethal(3)malignant brain tumor-like protein 3

Homo sapiens

UniProt Q96JM7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Sterile alpha motif domain-containing protein 1 × 2 （Q6SPF0） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Sterile alpha motif domain-containing protein 1 × 1 （Q6SPF0） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LMBL3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–73； UniProt 705–775

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	8y77
Deposition date deposition_date	2024-02-04
Structure title title	Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains
Keywords keywords	epigenetics, complex, polymer, CpG islands, GENE REGULATION; GENE REGULATION
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.

8y77__assembly_1__model_1

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

Download this curve (.dat)

8y77__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8y77__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.16 Å
Rg (electron density)	26.19 Å
Total Rg	26.54 Å
Atom count	2168
Residues	274
Excluded volume	38926 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8y77__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8y77__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Sterile alpha motif domain-containing protein 1
Molecular weight formula_weight	7541.6 kDa
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	1262

SPVEWTVMDVVEYFTEAGFPEQATAFQEQEIDGKSLLRMQRTDVLTGLSIRLGPALKIYEHHIKVL

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	Lethal(3)malignant brain tumor-like protein 3
Molecular weight formula_weight	8161.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSVSKWSTDEVSEFIQSLPGCEEHGKVFKDEQIDGEAFLLMTQTDIVKIMSIKEGPAEKIFNSILMFKAAEKN

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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Unit-cell length a length_a	43.981 Å
Unit-cell length b length_b	95.515 Å
Unit-cell length c length_c	65.926 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	24.020 Å
R factor r_factor	0.1846
R_work r_work	0.1835
R_free r_free	0.2078

Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains

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

Sterile alpha motif domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Lethal(3)malignant brain tumor-like protein 3

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

8y77__assembly_1__model_1

8y77__assembly_1__model_1 | I(q)

8y77__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains

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

Sterile alpha motif domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lethal(3)malignant brain tumor-like protein 3

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

8y77__assembly_1__model_1

8y77__assembly_1__model_1 | I(q)

8y77__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)