SAXSdb — 8ftu

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

Protein transport protein SEC39

Kluyveromyces lactis NRRL Y-1140

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Vesicle transport protein USE1 × 1 （Q6CL08） Protein transport protein DSL1 × 1 （Q6CUS2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CWC7_KLULA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 28–699； UniProt 1–672

Vesicle transport protein USE1

Kluyveromyces lactis NRRL Y-1140

UniProt Q6CL08

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC39 × 1 （Q6CWC7） Protein transport protein DSL1 × 1 （Q6CUS2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CL08_KLULA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–113； UniProt 1–110

Protein transport protein DSL1

Kluyveromyces lactis NRRL Y-1140

UniProt Q6CUS2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC39 × 1 （Q6CWC7） Vesicle transport protein USE1 × 1 （Q6CL08）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CUS2_KLULA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–38； UniProt 332–366 Author chain C； PDBConstruct 44–306； UniProt 424–686

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	8ftu
Deposition date deposition_date	2023-01-13
Structure title title	Crystal structure of the SNARE Use1 bound to Dsl1 complex subunits Sec39 and Dsl1, Revised Use1 structure
Keywords keywords	membrane trafficking, SNARE protein, COPI, vesicle, multisubunit tethering complex, Dsl1 complex, CATCHR complex, TRANSPORT PROTEIN; TRANSPORT 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.

8ftu__assembly_1__model_1

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

Download this curve (.dat)

8ftu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ftu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	71.61 Å
Rg (electron density)	72.54 Å
Total Rg	72.20 Å
Atom count	8254
Residues	1012
Excluded volume	148490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ftu__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Protein transport protein SEC39
Molecular weight formula_weight	79860.9 kDa
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	8254

MKHHHHHHHGAAGTSLYKKAGLVPRGSMNPQLYLCASVFITRGDVKSVSEIYQGLQSDAERLQYLKLLCVMWPELDAPTNISFVLKDIELNGMDESSVLVSLIQEDSSLTAISEMDVNTISKRVNALASYVEETLIGFNIHIRETHMLEDFIRARTLVVNSLSKDALCSLELLANSTSKSLVSWLDGILKPLDHLNRRLDTKLSIFQFENLSAQDAVSEMWKLPVKEVSVVRSMMKYEVEPYLKFQGSYTPFYEVIFNPDNFPLDSINNFQIYKYLSSQPTPLDTKFNETKWNILYSNGKNLASIPLPNLVFELESLIKSFGDDSQIFSGISLNEWLVNLKFMNAMDIKDLKSLKKLQNEDSVVQTSYFSIITQNMFQGHIDIKTVQNVVEFIESSTLFDKLTNELQTSILLESLLKLGKFDILEQFVSTSGVKIQDKVIIQHFWRFFNIASNGSLSDPDMKNANRTLNLLSNKETHSNLYDILTIVDRLSHYSLSFKRGMPFKPAHISEFKANPMEIVEKLLDLNPKLRKNIEVTFDILKELYTALQVTPSDKDFTKEYSKLLSEHINNLLANGDFKFAFDQAINLIERPDAAEHWVTIFQVGKYIDPNWLDAEIPTEIIYLQLGIVSKLLHICPEKEYEVITSQWSGLELELSTRNLISDKYSLENTQRSNDNFMSDVSTNVGNFLSGKFQWNIGGA

Source Source

Source organism organism	Kluyveromyces lactis NRRL Y-1140
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Vesicle transport protein USE1
Molecular weight formula_weight	13260.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSMTTDLDTLSDQLRKNYYRDLSLFQDDEDPFYHYLISTKLATNLNTVRKLAIKDNLDDPSSDAIDRYQKNFSRLEESVSSISFSKASKLQQKYDAYQESQKKRRYSVDFDA

Source Source

Source organism organism	Kluyveromyces lactis NRRL Y-1140
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Protein transport protein DSL1
Molecular weight formula_weight	36014.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSENIYTTLKFESMMQQRVIQIRSIPEEEYHELVSVQGDGDGPIQVSVFVQSAAKVFTEFEQGCDTIGRSKVESIYLYKFNLLQTAFFAMVSEKVNDWTQLYKDVRYLYTENPKLLQLMELNSRRLDLNLNLIKKTIYKLVNDQLQELKDNERTPDWDITISSLLPYLKKTALPTLYKLEDNTILVALIRYIVHDLVIDNILHWRVISEKSSENLSEFIMLLLSGLEIPRLNLIETYRHSREKLGILSKILTAHLKDILEMFYEGEFFLFETDEIVQWIILLFADTPTRRDCIDEIRRVREEATD

Source Source

Source organism organism	Kluyveromyces lactis NRRL Y-1140
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Escherichia coli BL21

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Unit-cell length a length_a	240.790 Å
Unit-cell length b length_b	87.846 Å
Unit-cell length c length_c	161.431 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	5.730 Å
Low-resolution limit resolution_low	29.600 Å
R factor r_factor	0.2782
R_work r_work	0.2759
R_free r_free	0.2980

Crystal structure of the SNARE Use1 bound to Dsl1 complex subunits Sec39 and Dsl1, Revised Use1 structure

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

Protein transport protein SEC39

State in the Current Structure

Other States of the Same Protein in the Database

Vesicle transport protein USE1

State in the Current Structure

Other States of the Same Protein in the Database

Protein transport protein DSL1

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

8ftu__assembly_1__model_1

8ftu__assembly_1__model_1 | I(q)

8ftu__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 polymer

Polymer Polymer

Source Source

7. Citations (2)

Crystal structure of the SNARE Use1 bound to Dsl1 complex subunits Sec39 and Dsl1, Revised Use1 structure

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

Protein transport protein SEC39

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vesicle transport protein USE1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein DSL1

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

8ftu__assembly_1__model_1

8ftu__assembly_1__model_1 | I(q)

8ftu__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 polymer

Polymer Polymer

Source Source

7. Citations (2)