SAXSdb — 4h8s

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

DCC-interacting protein 13-beta

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DP13B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–407； UniProt 2–384 Author chain B； PDBConstruct 25–407； UniProt 2–384 Author chain C； PDBConstruct 25–407； UniProt 2–384 Author chain D； PDBConstruct 25–407； UniProt 2–384

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	4h8s
Deposition date deposition_date	2012-09-23
Structure title title	Crystal structure of human APPL2BARPH domain
Keywords keywords	BAR domain, pleckstrin homology domain, adaptor protein, Rab binding, SIGNALING PROTEIN; SIGNALING 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.

4h8s__assembly_1__model_1

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

Download this curve (.dat)

4h8s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4h8s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.83 Å
Rg (electron density)	50.86 Å
Total Rg	50.70 Å
Atom count	11908
Residues	752
Excluded volume	106210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4h8s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4h8s__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 (1)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4h8sA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4h8sA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	4h8sB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4h8sB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	4h8sC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4h8sC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	4h8sD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4h8sD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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Unit-cell length a length_a	97.960 Å
Unit-cell length b length_b	208.013 Å
Unit-cell length c length_c	218.359 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	46.950 Å
R factor r_factor	0.2116
R_work r_work	0.2092
R_free r_free	0.2559

Description description	DCC-interacting protein 13-beta
Molecular weight formula_weight	46121.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	23866

Crystal structure of human APPL2BARPH domain

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

DCC-interacting protein 13-beta

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

4h8s__assembly_1__model_1

4h8s__assembly_1__model_1 | I(q)

4h8s__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Crystal structure of human APPL2BARPH domain

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

DCC-interacting protein 13-beta

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

4h8s__assembly_1__model_1

4h8s__assembly_1__model_1 | I(q)

4h8s__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)