SAXSdb — 2zii

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

Vacuolar protein sorting-associated protein 74

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS74_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–288； UniProt 60–345 Author chain B； PDBConstruct 3–288； UniProt 60–345 Author chain C； PDBConstruct 3–288； UniProt 60–345 Author chain D； PDBConstruct 3–288； UniProt 60–345

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	2zii
Deposition date deposition_date	2008-02-18
Structure title title	Crystal Structure of Yeast Vps74-N-term Truncation Variant
Keywords keywords	beta hairpin, vps, golgi localization, vps74, tetramer, Golgi apparatus, Phosphoprotein, Protein transport, 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.

2zii__assembly_1__model_1

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

Download this curve (.dat)

2zii__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zii__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.02 Å
Rg (electron density)	36.49 Å
Total Rg	36.71 Å
Atom count	8588
Residues	1124
Excluded volume	153410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zii__assembly_1__model_1`	tetrameric （4）	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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2ziiA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3630 — yeast vps74-n-term truncation variant fold
Homologous superfamily homologous superfamily	10 — yeast vps74-n-term truncation variant domain like

Domain ID domain_id	2ziiB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3630 — yeast vps74-n-term truncation variant fold
Homologous superfamily homologous superfamily	10 — yeast vps74-n-term truncation variant domain like

Domain ID domain_id	2ziiC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3630 — yeast vps74-n-term truncation variant fold
Homologous superfamily homologous superfamily	10 — yeast vps74-n-term truncation variant domain like

Domain ID domain_id	2ziiD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3630 — yeast vps74-n-term truncation variant fold
Homologous superfamily homologous superfamily	10 — yeast vps74-n-term truncation variant domain like

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Unit-cell length a length_a	104.081 Å
Unit-cell length b length_b	104.081 Å
Unit-cell length c length_c	292.759 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	3.050 Å
Low-resolution limit resolution_low	49.100 Å
R factor r_factor	0.2230
R_work r_work	0.2200
R_free r_free	0.2810

Description description	Vacuolar protein sorting-associated protein 74
Molecular weight formula_weight	33051.0 kDa
Mutation mutation	deletion of amino acids 1-59
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8590

Crystal Structure of Yeast Vps74-N-term Truncation Variant

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

Vacuolar protein sorting-associated protein 74

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

2zii__assembly_1__model_1

2zii__assembly_1__model_1 | I(q)

2zii__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

Crystal Structure of Yeast Vps74-N-term Truncation Variant

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

Vacuolar protein sorting-associated protein 74

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

2zii__assembly_1__model_1

2zii__assembly_1__model_1 | I(q)

2zii__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)