SAXSdb — 2v6x

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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 2	DOA4-INDEPENDENT DEGRADATION PROTEIN 4 × 1 （P36108） SULFATE ION × 1 water × 2	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 4–85； UniProt 1–82

DOA4-INDEPENDENT DEGRADATION PROTEIN 4

SACCHAROMYCES CEREVISIAE

UniProt P36108

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 4 × 1 （P52917） SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DID4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–54； UniProt 102–151

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	2v6x
Deposition date deposition_date	2007-07-23
Structure title title	Stractural insight into the interaction between ESCRT-III and Vps4
Keywords keywords	;PROTEIN TRANSPORT, VACUOLE, ENDOSOME, TRANSPORT, ESCRT-III, MVB, VPS2, VPS4, SKD1, VPS4B, VPS4A, CHMP2B, CHMP2A, NUCLEOTIDE-BINDING, AAA-ATPASE, ATP-BINDING, MULTIVESICULAR, VACUOLAR PROTEIN SORTING ;; 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.

2v6x__assembly_1__model_1

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

Download this curve (.dat)

2v6x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v6x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.98 Å
Rg (electron density)	15.64 Å
Total Rg	17.09 Å
Atom count	984
Residues	119
Excluded volume	17523 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v6x__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 (4)

Entity 1 Entity 1 polymer

Description description	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
Molecular weight formula_weight	9816.7 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1016

GSHMSTGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLMLALKYEKNPKSKDLIRAKFTEYLNRAEQLKKHLESEEANAA

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(DE3)

Entity 2 Entity 2 polymer

Description description	DOA4-INDEPENDENT DEGRADATION PROTEIN 4
Molecular weight formula_weight	5772.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMLQSTPQNLVSNAPIAETAMGIAEPIGAGSEFHGNPDDDLQARLNTLKKQT

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(DE3)

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2v6xa1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.14 — MIT domain
Family Family family	a.7.14.0 — automated matches

Domain ID domain_id	d2v6xa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2v6xA00
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	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

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Unit-cell length a length_a	78.145 Å
Unit-cell length b length_b	82.270 Å
Unit-cell length c length_c	21.474 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	56.610 Å
R factor r_factor	0.2000
R_work r_work	0.1980
R_free r_free	0.2280

Stractural insight into the interaction between ESCRT-III and Vps4

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

DOA4-INDEPENDENT DEGRADATION PROTEIN 4

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

2v6x__assembly_1__model_1

2v6x__assembly_1__model_1 | I(q)

2v6x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Stractural insight into the interaction between ESCRT-III and Vps4

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

DOA4-INDEPENDENT DEGRADATION 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2v6x__assembly_1__model_1

2v6x__assembly_1__model_1 | I(q)

2v6x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)