4riq

Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI)

Method: X-RAY DIFFRACTION

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

Protein dpy-30 homolog

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	Set1/Ash2 histone methyltransferase complex subunit ASH2 × 4 （Q9UBL3） SULFATE ION × 4 water × 7	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	Set1/Ash2 histone methyltransferase complex subunit ASH2 × 4 （Q9UBL3） SULFATE ION × 4 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPY30_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–56； UniProt 45–99 Author chain B； PDBConstruct 2–56； UniProt 45–99 Author chain D； PDBConstruct 2–56； UniProt 45–99 Author chain E； PDBConstruct 2–56； UniProt 45–99 Author chain G； PDBConstruct 2–56； UniProt 45–99 Author chain H； PDBConstruct 2–56； UniProt 45–99 Author chain J； PDBConstruct 2–56； UniProt 45–99 Author chain K； PDBConstruct 2–56； UniProt 45–99 Author chain M； PDBConstruct 2–56； UniProt 45–99 Author chain N； PDBConstruct 2–56； UniProt 45–99 Author chain P； PDBConstruct 2–56； UniProt 45–99 Author chain Q； PDBConstruct 2–56； UniProt 45–99 Author chain S； PDBConstruct 2–56； UniProt 45–99 Author chain T； PDBConstruct 2–56； UniProt 45–99 Author chain V； PDBConstruct 2–56； UniProt 45–99 Author chain Z； PDBConstruct 2–56； UniProt 45–99

Set1/Ash2 histone methyltransferase complex subunit ASH2

Homo sapiens

UniProt Q9UBL3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Protein dpy-30 homolog × 8 （Q9C005） SULFATE ION × 4 water × 7	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	Protein dpy-30 homolog × 8 （Q9C005） SULFATE ION × 4 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASH2L_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–21； UniProt 603–618 Author chain F； PDBConstruct 6–21； UniProt 603–618 Author chain I； PDBConstruct 6–21； UniProt 603–618 Author chain L； PDBConstruct 6–21； UniProt 603–618 Author chain O； PDBConstruct 6–21； UniProt 603–618 Author chain R； PDBConstruct 6–21； UniProt 603–618 Author chain U； PDBConstruct 6–21； UniProt 603–618 Author chain X； PDBConstruct 6–21； UniProt 603–618

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	4riq
Deposition date deposition_date	2014-10-07
Structure title title	Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI)
Keywords keywords	;histone, chromatin, methylation, dimerization/docking module, allosteric regulator, Ash2L, WDR5, RbBP5, MLL1, MLL2, MLL3, MLL4, SET1A, SET1B, 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.

4riq__assembly_1__model_1

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

Download this curve (.dat)

4riq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4riq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.56 Å
Rg (electron density)	22.70 Å
Total Rg	23.54 Å
Atom count	3710
Residues	489
Excluded volume	67175 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4riq__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4riq__assembly_2__model_1`	dodecameric （12）	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	Protein dpy-30 homolog
Molecular weight formula_weight	6300.3 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,G,H,J,K,M,N,P,Q,S,T,V,Z
Atom count atom_count	7461

GKVDLQSLPTRAYLDQTVVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN

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	Set1/Ash2 histone methyltransferase complex subunit ASH2
Molecular weight formula_weight	3054.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L,O,R,U,X

GAMGSVEHTLADVLYHVETEVENLYFQ

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	4riqA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqN00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqP00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqQ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqS00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqT00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqV00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	4riqZ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

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Unit-cell length a length_a	56.270 Å
Unit-cell length b length_b	56.270 Å
Unit-cell length c length_c	95.090 Å
Unit-cell angle α angle_alpha	90.08 °
Unit-cell angle β angle_beta	89.90 °
Unit-cell angle γ angle_gamma	115.39 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.231 Å
Low-resolution limit resolution_low	28.675 Å
R factor r_factor	0.2382
R_work r_work	0.2357
R_free r_free	0.2839

Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI)

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

Protein dpy-30 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Set1/Ash2 histone methyltransferase complex subunit ASH2

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

4riq__assembly_1__model_1

4riq__assembly_1__model_1 | I(q)

4riq__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI)

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

Protein dpy-30 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Set1/Ash2 histone methyltransferase complex subunit ASH2

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

4riq__assembly_1__model_1

4riq__assembly_1__model_1 | I(q)

4riq__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)