SAXSdb — 3k8p

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

Dsl1

Kluyveromyces lactis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein transport protein SEC39 × 1 （Q12745） water × 1	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	1
Chains and sequence ranges	Author chain C； PDBConstruct 3–357； UniProt 332–686

Protein transport protein SEC39

Saccharomyces cerevisiae

UniProt Q12745

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Dsl1 × 1 （Q6CUS2） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC39_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–709； UniProt 1–709

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	3k8p
Deposition date deposition_date	2009-10-14
Structure title title	Structural basis for vesicle tethering by the Dsl1 complex
Keywords keywords	;Intracellular trafficking, Dsl1 complex, multisubunit tethering complex, SNARE proteins, Endoplasmic reticulum, ER-Golgi transport, Membrane, Protein transport, Transport, TRANSPORT PROTEIN-TRANSPORT PROTEIN 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.

3k8p__assembly_1__model_1

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

Download this curve (.dat)

3k8p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k8p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	61.34 Å
Rg (electron density)	64.21 Å
Total Rg	63.31 Å
Atom count	7373
Residues	869
Excluded volume	133260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k8p__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 (3)

Entity 1 Entity 1 polymer

Description description	Dsl1
Molecular weight formula_weight	42387.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	7376

GSENIYTTLKFESMMQQRVIQIRSIPEEEYHELVSVQFKTDGGKYEKGEKQDLELSEKKTENGKDTESWGWNENQDSDEHDGWDEELDIDVDNVPIQVSVFVQSAAKVFTEFEQGCDTIGRSKVESIYLYKFNLLQTAFFAMVSEKVNDWTQLYKDVRYLYTENPKLLQLMELNSRRLDLNLNLIKKTIYKLVNDQLQELKDNERTPDWDITISSLLPYLKKTALPTLYKLEDNTILVALIRYIVHDLVIDNILHWRVISEKSSENLSEFIMLLLSGLEIPRLNLIETYRHSREKLGILSKILTAHLKDILEMFYEGEFFLFETDEIVQWIILLFADTPTRRDCIDEIRRVREEATD

Source Source

Source organism organism	Kluyveromyces lactis
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	28985
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein transport protein SEC39
Molecular weight formula_weight	83234.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLEEQLYLLACIFASRADTRNIKKLSTRLGSQSKYLEILCVLWPELDDPKNLLFLRELEEEVQSPEGEETTDEDVIVELLESDSSLIPLIESDTTTRSNRYHELQEFISKKLNNKTLENFEEWLRERILICNEMIPETPLLYSVLWETAKSKVLSTKFIGWVEGVLKPLDHLNKRLHLIFKINEWEKMPDSELFKIIFDGVEDMQGYIGIADVIEDELAPTLSYGKKWETFITEFFNKQQFSLKSDTNYQLFIKLYYSLEKGVKDNSEASRKLQSNVVDILFHNSENLFNLSSLTHKLDELWSILSGFPDEITIEEQKTITALEMKQFMEFFIKCSTKFSFKEIFAITQEEESAQLAHFSSLCHEEFNKANEISSFLQAMYETVLDISKDDKIFTRISMDEKLYSILEILLQMNEFAYIEAIIERFDYSNNTQIYELLVKFFWHFFNNASNGLRKEPEMKKASQTLQIIQKHMSQRAGTNLTKLEVLLEISDKLSHYSINLNKSHNGARDTAFKPSNILEYRDCPLDIISNLLELNPRLYKDLPTTKSLLFGIYDSLSINREGQTGKVEVDLMVLHIDYALVNLDFGTAYELGKQVFEICQEAGQHMMKALGDEHWLTFYQMGKFVDPNWVDNEIPTEIIVLQMSILGRLLEVCPLEEVEIVTSQWSTLELELSARDLVKDKYALDGQNDNKSKVGGIAREIFHNVTNF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3k8pC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1440 —

Domain ID domain_id	3k8pC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	150 —

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Unit-cell length a length_a	72.020 Å
Unit-cell length b length_b	90.820 Å
Unit-cell length c length_c	213.880 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	2.600 Å
Low-resolution limit resolution_low	31.197 Å
R factor r_factor	0.2082
R_work r_work	0.2049
R_free r_free	0.2708

Structural basis for vesicle tethering by the Dsl1 complex

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

Dsl1

State in the Current Structure

Other States of the Same Protein in the Database

Protein transport protein SEC39

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

3k8p__assembly_1__model_1

3k8p__assembly_1__model_1 | I(q)

3k8p__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structural basis for vesicle tethering by the Dsl1 complex

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3k8p__assembly_1__model_1

3k8p__assembly_1__model_1 | I(q)

3k8p__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)