SAXSdb — 5xmk

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

Vacuolar protein sorting-associated protein 4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Vacuolar protein sorting-associated protein VTA1 × 8 （Q06263） ADENOSINE-5'-TRIPHOSPHATE × 5	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 1–437； UniProt 1–437 Author chain B； PDBConstruct 1–437； UniProt 1–437 Author chain C； PDBConstruct 1–437； UniProt 1–437 Author chain D； PDBConstruct 1–437； UniProt 1–437 Author chain E； PDBConstruct 1–437； UniProt 1–437 Author chain F； PDBConstruct 1–437； UniProt 1–437

Vacuolar protein sorting-associated protein VTA1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06263

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Vacuolar protein sorting-associated protein 4 × 6 （P52917） ADENOSINE-5'-TRIPHOSPHATE × 5	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	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–330； UniProt 1–330 Author chain H； PDBConstruct 1–330； UniProt 1–330 Author chain I； PDBConstruct 1–330； UniProt 1–330 Author chain J； PDBConstruct 1–330； UniProt 1–330 Author chain K； PDBConstruct 1–330； UniProt 1–330 Author chain L； PDBConstruct 1–330； UniProt 1–330 Author chain M； PDBConstruct 1–330； UniProt 1–330 Author chain N； PDBConstruct 1–330； UniProt 1–330

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	5xmk
Deposition date deposition_date	2017-05-15
Structure title title	Cryo-EM structure of the ATP-bound Vps4 mutant-E233Q complex with Vta1 (masked)
Keywords keywords	ATPase, ESCRTIII, Vps4, Vta1, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

5xmk__assembly_1__model_1

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

Download this curve (.dat)

5xmk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xmk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.84 Å
Rg (electron density)	47.62 Å
Total Rg	47.83 Å
Atom count	18017
Residues	2298
Excluded volume	321180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xmk__assembly_1__model_1`	tetradecameric （14）	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	Vacuolar protein sorting-associated protein 4
Molecular weight formula_weight	48232.2 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	18017

MSTGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLMLALKYEKNPKSKDLIRAKFTEYLNRAEQLKKHLESEEANAAKKSPSAGSGSNGGNKKISQEEGEDNGGEDNKKLRGALSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEGN

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein VTA1
Molecular weight formula_weight	37359.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L,M,N

MASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIGGESEAEDSDKSLHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIGSSDEKTLDYADFADDSEEIKDEDVDHQTSDLENNNNDKVEGLAPKDQTTSYEPVDEVPEFIDDADSVNEEEQTVDKNEDAITKDEQQVVKKEVDLTRPSAPSEPAAAEHKSYTKDELTKIMDRASKIEQIQKLAKYAISALNYEDLPTAKDELTKALDLLNSI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	5

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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	1

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

Resolution resolution	4.180 Å
Low-resolution limit resolution_low	166.320 Å
R factor r_factor	0.3547
R_work r_work	0.3547
R_free r_free	—

Resolution resolution	4.18 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	106106

Cryo-EM structure of the ATP-bound Vps4 mutant-E233Q complex with Vta1 (masked)

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

5xmk__assembly_1__model_1

5xmk__assembly_1__model_1 | I(q)

5xmk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)

Cryo-EM structure of the ATP-bound Vps4 mutant-E233Q complex with Vta1 (masked)

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

5xmk__assembly_1__model_1

5xmk__assembly_1__model_1 | I(q)

5xmk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)