SAXSdb — 2vpd

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

PYGOPUS HOMOLOG 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 2	B-CELL CLL/LYMPHOMA 9 PROTEIN × 1 （O00512） ZINC ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	B-CELL CLL/LYMPHOMA 9 PROTEIN × 1 （O00512） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYGO1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–67； UniProt 333–398 Author chain C； PDBConstruct 2–67； UniProt 333–398

B-CELL CLL/LYMPHOMA 9 PROTEIN

HOMO SAPIENS

UniProt O00512

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PYGOPUS HOMOLOG 1 × 1 （Q9Y3Y4） ZINC ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PYGOPUS HOMOLOG 1 × 1 （Q9Y3Y4） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCL9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–35； UniProt 174–205 Author chain D； PDBConstruct 4–35； UniProt 174–205

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	2vpd
Deposition date deposition_date	2008-02-27
Structure title title	Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
Keywords keywords	;GENE REGULATION, WNT SIGNALING PATHWAY, WNT SIGNALING COMPLEX, CHROMOSOMAL REARRANGEMENT, SIGNALING PROTEIN, BCL9 HD1 DOMAIN, HPYGO1 PHD DOMAIN, PROTO-ONCOGENE, PHOSPHOPROTEIN, HISTONE H3K4ME2, ZINC, NUCLEUS, ZINC-FINGER, METAL-BINDING ;; 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.

2vpd__assembly_2__model_1

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

Download this curve (.dat)

2vpd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vpd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.46 Å
Rg (electron density)	14.42 Å
Total Rg	15.51 Å
Atom count	754
Residues	101
Excluded volume	13396 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vpd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vpd__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	PYGOPUS HOMOLOG 1
Molecular weight formula_weight	7229.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1473

MGHSSSDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCMAD

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	B-CELL CLL/LYMPHOMA 9 PROTEIN
Molecular weight formula_weight	3758.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AMAAKVVYVFSTEMANKAAEAVLKGQVETIVSFHI

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vpdA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	2vpdC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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Unit-cell length a length_a	88.720 Å
Unit-cell length b length_b	100.890 Å
Unit-cell length c length_c	64.240 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	66.670 Å
R factor r_factor	0.2350
R_work r_work	0.2340
R_free r_free	0.2670

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex

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

PYGOPUS HOMOLOG 1

State in the Current Structure

Other States of the Same Protein in the Database

B-CELL CLL/LYMPHOMA 9 PROTEIN

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

2vpd__assembly_2__model_1

2vpd__assembly_2__model_1 | I(q)

2vpd__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex

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

PYGOPUS HOMOLOG 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

B-CELL CLL/LYMPHOMA 9 PROTEIN

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

2vpd__assembly_2__model_1

2vpd__assembly_2__model_1 | I(q)

2vpd__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)