SAXSdb — 5yca

▼

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

Ubiquitin-like protein SMT3,Bouquet formation protein 4

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Lap-Emerin-Man domain protein 2 × 1 （Q10109） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BQT4_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 75–207； UniProt 8–140

Ubiquitin-like protein SMT3,Bouquet formation protein 4

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Lap-Emerin-Man domain protein 2 × 1 （Q10109） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–74； UniProt 20–92

Lap-Emerin-Man domain protein 2

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt Q10109

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Ubiquitin-like protein SMT3,Bouquet formation protein 4 × 1 （O60158,Q12306） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEM2_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–20； UniProt 261–279

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5yca
Deposition date deposition_date	2017-09-07
Structure title title	Crystal structure of inner membrane protein Bqt4 in complex with LEM2
Keywords keywords	Chromosome organization, Membrane organization, Bouquet formation, Lap-Emerin-Man domain protein, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5yca__assembly_1__model_1

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

Download this curve (.dat)

5yca__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yca__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.65 Å
Rg (electron density)	21.12 Å
Total Rg	21.86 Å
Atom count	1774
Residues	223
Excluded volume	31412 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yca__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein SMT3,Bouquet formation protein 4
Molecular weight formula_weight	23570.9 kDa
Mutation mutation	Q61E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2077

GPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIEADQTPEDLDMEDNDIIEAHRSLPAERNPLYKDDTLDHTPLIPKCRAQVIEFPDGPATFVRLKCTNPESKVPHFLMRMAKDSSISATSMFRSAFPKATQEEEDLEMRWIRDNLNPIEDKRVAGLWVPPADALALAKDYSMTPFINALLEASST

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Lap-Emerin-Man domain protein 2
Molecular weight formula_weight	2372.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSAEEDDELFQNYVLQQTRK

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	294

▶

Unit-cell length a length_a	43.868 Å
Unit-cell length b length_b	53.128 Å
Unit-cell length c length_c	109.566 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	27.392 Å
R factor r_factor	0.1906
R_work r_work	0.1894
R_free r_free	0.2136

Crystal structure of inner membrane protein Bqt4 in complex with LEM2

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

Ubiquitin-like protein SMT3,Bouquet formation protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,Bouquet formation protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Lap-Emerin-Man domain protein 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

5yca__assembly_1__model_1

5yca__assembly_1__model_1 | I(q)

5yca__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of inner membrane protein Bqt4 in complex with LEM2

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

Ubiquitin-like protein SMT3,Bouquet formation protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,Bouquet formation protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lap-Emerin-Man domain 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5yca__assembly_1__model_1

5yca__assembly_1__model_1 | I(q)

5yca__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)