SAXSdb — 6oo2

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

Vacuolar protein sorting-associated protein 4

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Designed Cyclic Peptide × 1 Vacuolar protein sorting-associated protein VTA1 × 12 （Q06263） ADENOSINE-5'-DIPHOSPHATE × 5 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–337； UniProt 101–437 Author chain B； PDBConstruct 1–337； UniProt 101–437 Author chain C； PDBConstruct 1–337； UniProt 101–437 Author chain D； PDBConstruct 1–337； UniProt 101–437 Author chain E； PDBConstruct 1–337； UniProt 101–437 Author chain F； PDBConstruct 1–337； UniProt 101–437

Vacuolar protein sorting-associated protein VTA1

Saccharomyces cerevisiae

UniProt Q06263

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Vacuolar protein sorting-associated protein 4 × 6 （P52917） Designed Cyclic Peptide × 1 ADENOSINE-5'-DIPHOSPHATE × 5 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VTA1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–51； UniProt 280–330 Author chain I； PDBConstruct 1–51； UniProt 280–330 Author chain J； PDBConstruct 1–51； UniProt 280–330 Author chain K； PDBConstruct 1–51； UniProt 280–330 Author chain L； PDBConstruct 1–51； UniProt 280–330 Author chain M； PDBConstruct 1–51； UniProt 280–330 Author chain N； PDBConstruct 1–51； UniProt 280–330 Author chain O； PDBConstruct 1–51； UniProt 280–330 Author chain P； PDBConstruct 1–51； UniProt 280–330 Author chain Q； PDBConstruct 1–51； UniProt 280–330 Author chain R； PDBConstruct 1–51； UniProt 280–330 Author chain S； PDBConstruct 1–51； UniProt 280–330

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	6oo2
Deposition date deposition_date	2019-04-22
Structure title title	Vps4 with Cyclic Peptide Bound in the Central Pore
Keywords keywords	Vps4, ESCRT, Vta1, AAA ATPase, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6oo2__assembly_1__model_1

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

Download this curve (.dat)

6oo2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6oo2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.16 Å
Rg (electron density)	47.30 Å
Total Rg	47.28 Å
Atom count	16691
Residues	2443
Excluded volume	290500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6oo2__assembly_1__model_1`	nonadecameric （19）	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 4
Molecular weight formula_weight	37120.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16691

QEEGEDNGGEDNKKLRGALSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDEVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEGN

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Designed Cyclic Peptide
Molecular weight formula_weight	2660.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GGDEIVNKVLGGSSGGXXXXXXXXGGKGCK

Entity 3 Entity 3 polymer

Description description	Vacuolar protein sorting-associated protein VTA1
Molecular weight formula_weight	5773.6 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J,K,L,M,N,O,P,Q,R,S

TKDELTKIMDRASKIEQIQKLAKYAISALNYEDLPTAKDELTKALDLLNSI

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	4.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	24778

Vps4 with Cyclic Peptide Bound in the Central Pore

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

Vacuolar protein sorting-associated protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein VTA1

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

6oo2__assembly_1__model_1

6oo2__assembly_1__model_1 | I(q)

6oo2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Vps4 with Cyclic Peptide Bound in the Central Pore

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

Vacuolar protein sorting-associated protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar protein sorting-associated protein VTA1

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

6oo2__assembly_1__model_1

6oo2__assembly_1__model_1 | I(q)

6oo2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)