SAXSdb — 8fud

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

Vacuolar protein sorting-associated protein 29

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Putative vacuolar protein sorting-associated protein × 1 （G0SH11） PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Putative vacuolar protein sorting-associated protein × 1 （G0SH11） GLYCEROL × 1 DIMETHYL SULFOXIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS29_MOUSE
Isoform	Q9QZ88-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–188； UniProt 1–186 Author chain B； PDBConstruct 3–188； UniProt 1–186

Putative vacuolar protein sorting-associated protein

OrganismNot specified

UniProt G0SH11

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Vacuolar protein sorting-associated protein 29 × 1 （Q9QZ88） PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Vacuolar protein sorting-associated protein 29 × 1 （Q9QZ88） GLYCEROL × 1 DIMETHYL SULFOXIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SH11_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 71–80 Author chain D； PDBConstruct 1–10； UniProt 71–80

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	8fud
Deposition date deposition_date	2023-01-17
Last revision last_revision	2024-07-24
Structure title title	Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)
Keywords keywords	Retromer, endosome, sorting nexin, membrane trafficking, Protein transport; 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.

8fud__assembly_1__model_1

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

Download this curve (.dat)

8fud__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8fud__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.87 Å
Rg (electron density)	15.53 Å
Total Rg	16.69 Å
Atom count	1532
Residues	193
Excluded volume	27478 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8fud__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8fud__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Vacuolar protein sorting-associated protein 29
Molecular weight formula_weight	21089.3 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	3441

GSMAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Putative vacuolar protein sorting-associated protein
Molecular weight formula_weight	983.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

EDDPLGPLGA

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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Unit-cell length a length_a	54.051 Å
Unit-cell length b length_b	68.597 Å
Unit-cell length c length_c	211.139 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	41.620 Å
R factor r_factor	0.1782
R_work r_work	0.1769
R_free r_free	0.2025

Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)

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

Vacuolar protein sorting-associated protein 29

State in the Current Structure

Other States of the Same Protein in the Database

Putative vacuolar protein sorting-associated protein

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

8fud__assembly_1__model_1

8fud__assembly_1__model_1 | I(q)

8fud__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)

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

Vacuolar protein sorting-associated protein 29

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative vacuolar protein sorting-associated protein

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

8fud__assembly_1__model_1

8fud__assembly_1__model_1 | I(q)

8fud__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)