SAXSdb — 9vn5

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

WD repeat-containing protein 5

Homo sapiens

UniProt P61964

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Methyl-CpG binding domain protein 3 × 1 （D3YTR4） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Methyl-CpG binding domain protein 3 × 1 （D3YTR4） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WDR5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–315； UniProt 24–334 Author chain B； PDBConstruct 5–315； UniProt 24–334

Methyl-CpG binding domain protein 3

Mus musculus

UniProt D3YTR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	WD repeat-containing protein 5 × 1 （P61964） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	WD repeat-containing protein 5 × 1 （P61964） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3YTR4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 76–85 Author chain D； PDBConstruct 1–10； UniProt 76–85

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	9vn5
Deposition date deposition_date	2025-06-30
Structure title title	Structure of WDR5 in complex with MBD3C R43K
Keywords keywords	WDR5, MBD3C, WIN motif, chromatin, NUCLEAR PROTEIN; NUCLEAR 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.

9vn5__assembly_1__model_1

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

Download this curve (.dat)

9vn5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vn5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.79 Å
Rg (electron density)	17.83 Å
Total Rg	18.88 Å
Atom count	2414
Residues	314
Excluded volume	43111 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vn5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9vn5__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	WD repeat-containing protein 5
Molecular weight formula_weight	34646.3 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	5056

GSHMTQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

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	Methyl-CpG binding domain protein 3
Molecular weight formula_weight	1037.2 kDa
Mutation mutation	R79K
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAAKCRVFSP

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
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	210

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Unit-cell length a length_a	116.265 Å
Unit-cell length b length_b	47.376 Å
Unit-cell length c length_c	129.472 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	43.300 Å
R factor r_factor	0.2065
R_work r_work	0.2052
R_free r_free	0.2311

Structure of WDR5 in complex with MBD3C R43K

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

WD repeat-containing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Methyl-CpG binding domain 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

9vn5__assembly_1__model_1

9vn5__assembly_1__model_1 | I(q)

9vn5__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)

Structure of WDR5 in complex with MBD3C R43K

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

WD repeat-containing protein 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

Methyl-CpG binding domain 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

9vn5__assembly_1__model_1

9vn5__assembly_1__model_1 | I(q)

9vn5__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)