SAXSdb — 1mi1

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

Neurobeachin

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NBEA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–414； UniProt 2150–2563 Author chain B； PDBConstruct 1–414； UniProt 2150–2563

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	1mi1
Deposition date deposition_date	2002-08-21
Structure title title	Crystal Structure of the PH-BEACH Domain of Human Neurobeachin
Keywords keywords	;PH domain, BEACH domain, vesicle trafficking, signal transduction, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

1mi1__assembly_1__model_1

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

Download this curve (.dat)

1mi1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mi1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.94 Å
Rg (electron density)	31.20 Å
Total Rg	31.74 Å
Atom count	6654
Residues	798
Excluded volume	118360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mi1__assembly_1__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

SCOP 2.08 (4 domains)

Domain ID domain_id	d1mi1a1
Class class	a — All alpha proteins
Fold Fold fold	a.169 — BEACH domain
Superfamily Superfamily superfamily	a.169.1 — BEACH domain
Family Family family	a.169.1.1 — BEACH domain

Domain ID domain_id	d1mi1a2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.6 — PreBEACH PH-like domain

Domain ID domain_id	d1mi1b1
Class class	a — All alpha proteins
Fold Fold fold	a.169 — BEACH domain
Superfamily Superfamily superfamily	a.169.1 — BEACH domain
Family Family family	a.169.1.1 — BEACH domain

Domain ID domain_id	d1mi1b2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.6 — PreBEACH PH-like domain

CATH v4.4 (4 domains)

Domain ID domain_id	1mi1A01
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	1mi1A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1540 — Neurobeachin; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — BEACH domain

Domain ID domain_id	1mi1B01
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	1mi1B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1540 — Neurobeachin; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — BEACH domain

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Unit-cell length a length_a	179.910 Å
Unit-cell length b length_b	179.910 Å
Unit-cell length c length_c	98.540 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	29.710 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2640

Description description	Neurobeachin
Molecular weight formula_weight	48216.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6654

Crystal Structure of the PH-BEACH Domain of Human Neurobeachin

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

Neurobeachin

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

1mi1__assembly_1__model_1

1mi1__assembly_1__model_1 | I(q)

1mi1__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

SCOP 2.08 (4 domains)

CATH v4.4 (4 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 the PH-BEACH Domain of Human Neurobeachin

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

Neurobeachin

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

1mi1__assembly_1__model_1

1mi1__assembly_1__model_1 | I(q)

1mi1__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

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)