SAXSdb — 8hib

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

LIM domain-binding 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 8	Single-stranded DNA-binding protein 2 × 4 （P81877） Pygopus homolog 2 × 2 （Q9BRQ0） water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDB1_HUMAN
Isoform	Q86U70-2
PDB entities	1
Chains and sequence ranges	Author chain V； PDBConstruct 1–230； UniProt 20–249

Single-stranded DNA-binding protein 2

Homo sapiens

UniProt P81877

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	LIM domain-binding protein 1 × 2 （Q86U70） Pygopus homolog 2 × 2 （Q9BRQ0） water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSBP2_HUMAN
Isoform	P81877-3
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 1–94 Author chain B； PDBConstruct 1–94； UniProt 1–94

Pygopus homolog 2

Homo sapiens

UniProt Q9BRQ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	LIM domain-binding protein 1 × 2 （Q86U70） Single-stranded DNA-binding protein 2 × 4 （P81877） water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYGO2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 2–27； UniProt 59–84

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	8hib
Deposition date deposition_date	2022-11-19
Structure title title	The crystal structure of Pygo2-LDB1-SSBP2 triple complex
Keywords keywords	Protein binding, Complex, TRANSCRIPTION; TRANSCRIPTION
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.

8hib__assembly_1__model_1

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

Download this curve (.dat)

8hib__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8hib__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.57 Å
Rg (electron density)	35.72 Å
Total Rg	35.90 Å
Atom count	6462
Residues	782
Excluded volume	114590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8hib__assembly_1__model_1`	octameric （8）	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	LIM domain-binding protein 1
Molecular weight formula_weight	27294.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V
Atom count atom_count	3298

GIGRHTPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPKRYTIGRTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQVCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGLSNSTLNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPP

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	Single-stranded DNA-binding protein 2
Molecular weight formula_weight	10863.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWCVFWDLYCAAPERRETCEHSSEAKAFHDY

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 polymer

Description description	Pygopus homolog 2
Molecular weight formula_weight	2966.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

YTEFAPPPTPMVDHLVASNPFEDDFGA

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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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Unit-cell length a length_a	104.499 Å
Unit-cell length b length_b	104.499 Å
Unit-cell length c length_c	252.274 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.2146
R_work r_work	0.2130
R_free r_free	0.2462

The crystal structure of Pygo2-LDB1-SSBP2 triple complex

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

LIM domain-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Single-stranded DNA-binding protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Pygopus homolog 2

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

8hib__assembly_1__model_1

8hib__assembly_1__model_1 | I(q)

8hib__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

7. Citations (1)

The crystal structure of Pygo2-LDB1-SSBP2 triple complex

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

LIM domain-binding 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

Single-stranded DNA-binding protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pygopus homolog 2

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

8hib__assembly_1__model_1

8hib__assembly_1__model_1 | I(q)

8hib__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

7. Citations (1)