SAXSdb — 5fjz

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

COATOMER SUBUNIT DELTA

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	PROTEIN TRANSPORT PROTEIN DSL1 × 4 （P53847） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COPD_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–270； UniProt 282–546 Author chain B； PDBConstruct 6–270； UniProt 282–546 Author chain C； PDBConstruct 6–270； UniProt 282–546 Author chain D； PDBConstruct 6–270； UniProt 282–546

PROTEIN TRANSPORT PROTEIN DSL1

OrganismNot specified

UniProt P53847

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	COATOMER SUBUNIT DELTA × 4 （P43621） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSL1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–9； UniProt 411–419 Author chain Q； PDBConstruct 1–9； UniProt 411–419 Author chain R； PDBConstruct 1–9； UniProt 411–419 Author chain S； PDBConstruct 1–9； UniProt 411–419

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	5fjz
Deposition date deposition_date	2015-10-14
Structure title title	Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide
Keywords keywords	PROTEIN TRANSPORT, COP-I, VESICLE COAT PROTEIN; PROTEIN TRANSPORT
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.

5fjz__assembly_1__model_1

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

Download this curve (.dat)

5fjz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fjz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.10 Å
Rg (electron density)	30.62 Å
Total Rg	31.44 Å
Atom count	8374
Residues	1070
Excluded volume	148580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fjz__assembly_1__model_1`	octameric （8）	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	COATOMER SUBUNIT DELTA
Molecular weight formula_weight	29783.2 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9030

GPLGSEEDVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTAVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PROTEIN TRANSPORT PROTEIN DSL1
Molecular weight formula_weight	1207.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R,S

DDWNWEVED

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	540

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Unit-cell length a length_a	72.810 Å
Unit-cell length b length_b	72.810 Å
Unit-cell length c length_c	343.290 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	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	36.400 Å
R factor r_factor	0.1466
R_work r_work	0.1445
R_free r_free	0.1861

Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide

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

COATOMER SUBUNIT DELTA

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

5fjz__assembly_1__model_1

5fjz__assembly_1__model_1 | I(q)

5fjz__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

Entity 3 Entity 3 water

7. Citations (1)

Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide

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

COATOMER SUBUNIT DELTA

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

5fjz__assembly_1__model_1

5fjz__assembly_1__model_1 | I(q)

5fjz__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

Entity 3 Entity 3 water

7. Citations (1)