SAXSdb — 4rnd

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

V-type proton ATPase subunit D

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	V-type proton ATPase subunit F × 2 （P39111） GLYCEROL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–256； UniProt 1–256 Author chain C； PDBConstruct 1–256； UniProt 1–256

V-type proton ATPase subunit F

Saccharomyces cerevisiae S288c

UniProt P39111

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	V-type proton ATPase subunit D × 2 （P32610） GLYCEROL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATF_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118 Author chain D； PDBConstruct 1–118； UniProt 1–118

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	4rnd
Deposition date deposition_date	2014-10-24
Structure title title	Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase.
Keywords keywords	alpha helical, Rossmann Fold, Hydrolase, Regulatory, Coupling; HYDROLASE
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.

4rnd__assembly_1__model_1

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

Download this curve (.dat)

4rnd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4rnd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.55 Å
Rg (electron density)	36.48 Å
Total Rg	36.61 Å
Atom count	4682
Residues	578
Excluded volume	83207 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase subunit D
Molecular weight formula_weight	29235.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4749

MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRVMQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDFRLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPRTENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEEPQGETLVADQEDDVIF

Source Source

Source organism organism	Saccharomyces cerevisiae 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	V-type proton ATPase subunit F
Molecular weight formula_weight	13479.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Source Source

Source organism organism	Saccharomyces cerevisiae 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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	59

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4rndb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.149 — AtpF-like
Superfamily Superfamily superfamily	c.149.1 — AtpF-like
Family Family family	c.149.1.1 — AtpF-like

Domain ID domain_id	d4rndd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.149 — AtpF-like
Superfamily Superfamily superfamily	c.149.1 — AtpF-like
Family Family family	c.149.1.1 — AtpF-like

CATH v4.4 (2 domains)

Domain ID domain_id	4rndB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10580 — ATPase, V1 complex, subunit F

Domain ID domain_id	4rndD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10580 — ATPase, V1 complex, subunit F

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Unit-cell length a length_a	168.063 Å
Unit-cell length b length_b	168.063 Å
Unit-cell length c length_c	128.629 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	29.630 Å
R factor r_factor	0.2045
R_work r_work	0.2036
R_free r_free	0.2320

Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase.

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

V-type proton ATPase subunit D

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit F

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

4rnd__assembly_1__model_1

4rnd__assembly_1__model_1 | I(q)

4rnd__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase.

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

V-type proton ATPase subunit D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit F

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

4rnd__assembly_1__model_1

4rnd__assembly_1__model_1 | I(q)

4rnd__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)