SAXSdb — 2fim

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

Tubby related protein 1

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	3-(N,N-DIMETHYLOCTYLAMMONIO)PROPANESULFONATE × 1 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TULP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–276； UniProt 290–542 Author chain B； PDBConstruct 24–276； UniProt 290–542

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	2fim
Deposition date deposition_date	2005-12-29
Structure title title	Structure of the C-terminal domain of Human Tubby-like protein 1
Keywords keywords	;TUBBY FILLED-BARREL, BETA-BARREL, FILLED-BETA-ROLL, 12-STRANDED-BETA-BARREL, HELIX-FILLED-BARREL, Retinitis pigmentosa, Blindness, STRUCTURAL GENOMICS, 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.

2fim__assembly_1__model_1

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

Download this curve (.dat)

2fim__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fim__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.90 Å
Rg (electron density)	25.91 Å
Total Rg	26.66 Å
Atom count	3711
Residues	456
Excluded volume	65913 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fim__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 (4)

Entity 1 Entity 1 polymer

Description description	Tubby related protein 1
Molecular weight formula_weight	31446.7 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	3841

MHHHHHHSSGVDLGTENLYFQSMEPREFVLRPAPQGRTVRCRLTRDKKGMDRGMYPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDPTNLSRGGENFIGKLRSNLLGNRFTVFDNGQNPQRGYSTNVASLRQELAAVIYETNVLGFRGPRRMTVIIPGMSAENERVPIRPRNASDGLLVRWQNKTLESLIELHNKPPVWNDDSGSYTLNFQGRVTQASVKNFQIVHADDPDYIVLQFGRVAEDAFTLDYRYPLCALQAFAIALSSFDGKLACE

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	3-(N,N-DIMETHYLOCTYLAMMONIO)PROPANESULFONATE
Molecular weight formula_weight	279.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2fima_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.23 — Tubby C-terminal domain-like
Superfamily Superfamily superfamily	d.23.1 — Tubby C-terminal domain-like
Family Family family	d.23.1.1 — Transcriptional factor tubby, C-terminal domain

Domain ID domain_id	d2fimb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.23 — Tubby C-terminal domain-like
Superfamily Superfamily superfamily	d.23.1 — Tubby C-terminal domain-like
Family Family family	d.23.1.1 — Transcriptional factor tubby, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	2fimA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	90 — Tubby Protein; Chain A
Homologous superfamily homologous superfamily	10 — Tubby Protein; Chain A

Domain ID domain_id	2fimB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	90 — Tubby Protein; Chain A
Homologous superfamily homologous superfamily	10 — Tubby Protein; Chain A

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Unit-cell length a length_a	55.960 Å
Unit-cell length b length_b	85.150 Å
Unit-cell length c length_c	58.790 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.890 Å
R factor r_factor	0.2010
R_work r_work	0.1990
R_free r_free	0.2350

Structure of the C-terminal domain of Human Tubby-like protein 1

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

Tubby related protein 1

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

2fim__assembly_1__model_1

2fim__assembly_1__model_1 | I(q)

2fim__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the C-terminal domain of Human Tubby-like protein 1

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

Tubby related 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2fim__assembly_1__model_1

2fim__assembly_1__model_1 | I(q)

2fim__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)