SAXSdb — 4uy4

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

SPINDLIN-4

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 H3K4ME3 × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3K4ME3 × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIN4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–216； UniProt 36–249 Author chain B； PDBConstruct 3–216； UniProt 36–249

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	4uy4
Deposition date deposition_date	2014-08-28
Structure title title	1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide
Keywords keywords	PEPTIDE BINDING PROTEIN, SPINDLIN MEMBER 4, SPIN4, TUDOR DOMAIN, EPIGENETIC, CYSTICERCOSIS, MENINGOENCEPHALITIS; PEPTIDE BINDING PROTEIN
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.

4uy4__assembly_1__model_1

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

Download this curve (.dat)

4uy4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4uy4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.17 Å
Rg (electron density)	17.64 Å
Total Rg	18.77 Å
Atom count	1693
Residues	213
Excluded volume	30178 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4uy4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4uy4__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 (4)

Entity 1 Entity 1 polymer

Description description	SPINDLIN-4
Molecular weight formula_weight	24882.3 kDa
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	3625

SMTRRNIVGCRIQHGWKEGNEPVEQWKGTVLEQVSVKPTLYIIKYDGKDSVYGLELHRDKRVLALEILPERVPTPRIDSRLADSLIGKAVEHVFEGEHGTKDEWKGMVLARAPVMDTWFYITYEKDPVLYMYTLLDDYKDGDLRIIPDSNYYFPTAEQEPGEVVDSLVGKQVEHAKDDGSKRTGIFIHQVVAKPSVYFIKFDDDIHIYVYGLVKTP

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 H3K4ME3
Molecular weight formula_weight	747.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

ARTKQT

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4uy4A00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	70 — Spindlin/Ssty

Domain ID domain_id	4uy4B00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	70 — Spindlin/Ssty

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Unit-cell length a length_a	39.072 Å
Unit-cell length b length_b	51.690 Å
Unit-cell length c length_c	57.141 Å
Unit-cell angle α angle_alpha	81.25 °
Unit-cell angle β angle_beta	89.89 °
Unit-cell angle γ angle_gamma	88.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.862 Å
Low-resolution limit resolution_low	28.683 Å
R factor r_factor	0.2033
R_work r_work	0.2016
R_free r_free	0.2350

1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide

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

SPINDLIN-4

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

4uy4__assembly_1__model_1

4uy4__assembly_1__model_1 | I(q)

4uy4__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide

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

SPINDLIN-4

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

4uy4__assembly_1__model_1

4uy4__assembly_1__model_1 | I(q)

4uy4__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)