4dl0

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase

Method: X-RAY DIFFRACTION

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

V-type proton ATPase subunit C

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	V-type proton ATPase subunit G × 1 （P48836） V-type proton ATPase subunit E × 1 （P22203） SULFATE ION × 4 TRIMETHYL LEAD ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	V-type proton ATPase subunit G × 1 （P48836） V-type proton ATPase subunit E × 1 （P22203） SULFATE ION × 4 TRIMETHYL LEAD ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 11–130； UniProt 158–277 Author chain I； PDBConstruct 11–130； UniProt 158–277

V-type proton ATPase subunit G

Saccharomyces cerevisiae

UniProt P48836

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit E × 1 （P22203） SULFATE ION × 4 TRIMETHYL LEAD ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit E × 1 （P22203） SULFATE ION × 4 TRIMETHYL LEAD ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATG_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 6–119； UniProt 1–114 Author chain K； PDBConstruct 6–119； UniProt 1–114

V-type proton ATPase subunit E

Saccharomyces cerevisiae

UniProt P22203

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit G × 1 （P48836） SULFATE ION × 4 TRIMETHYL LEAD ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit G × 1 （P48836） SULFATE ION × 4 TRIMETHYL LEAD ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATE_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–233； UniProt 1–233 Author chain J； PDBConstruct 1–233； UniProt 1–233

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	4dl0
Deposition date deposition_date	2012-02-05
Structure title title	Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase
Keywords keywords	coiled-coil, heterotrimer, peripheral stalk, stator complex, hydrolase, ion transport, Vacuolar ATPase, vacuolar membrane; 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.

4dl0__assembly_1__model_1

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

Download this curve (.dat)

4dl0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dl0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	61.81 Å
Rg (electron density)	64.37 Å
Total Rg	63.50 Å
Atom count	3527
Residues	441
Excluded volume	63271 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dl0__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4dl0__assembly_2__model_1`	trimeric （3）	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	V-type proton ATPase subunit C
Molecular weight formula_weight	14586.5 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,C
Atom count atom_count	7135

GPKVPESGSMNLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	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 G
Molecular weight formula_weight	13218.3 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,G

GPKVPMSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit E
Molecular weight formula_weight	26508.4 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,E

MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	TRIMETHYL LEAD ION
Molecular weight formula_weight	252.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4dl0e1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.36 — V-type ATPase peripheral stalk subunit E coiled coil
Family Family family	h.1.36.1 — V-type ATPase peripheral stalk subunit E coiled coil

Domain ID domain_id	d4dl0e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.4 — V-type ATPase subunit E-like
Family Family family	d.81.4.1 — V-type ATPase subunit E C-terminal domain

Domain ID domain_id	d4dl0g_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.37 — V-type ATPase peripheral stalk subunit G coiled coil
Family Family family	h.1.37.1 — V-type ATPase peripheral stalk subunit G coiled coil

Domain ID domain_id	d4dl0j1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.36 — V-type ATPase peripheral stalk subunit E coiled coil
Family Family family	h.1.36.1 — V-type ATPase peripheral stalk subunit E coiled coil

Domain ID domain_id	d4dl0j2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.4 — V-type ATPase subunit E-like
Family Family family	d.81.4.1 — V-type ATPase subunit E C-terminal domain

Domain ID domain_id	d4dl0k_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.37 — V-type ATPase peripheral stalk subunit G coiled coil
Family Family family	h.1.37.1 — V-type ATPase peripheral stalk subunit G coiled coil

CATH v4.4 (6 domains)

Domain ID domain_id	4dl0C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	4dl0E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	4dl0G00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2950 —

Domain ID domain_id	4dl0I00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	4dl0J02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	4dl0K00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2950 —

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Unit-cell length a length_a	95.790 Å
Unit-cell length b length_b	105.611 Å
Unit-cell length c length_c	120.486 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.905 Å
Low-resolution limit resolution_low	39.710 Å
R factor r_factor	0.2115
R_work r_work	0.2078
R_free r_free	0.2569

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase

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

V-type proton ATPase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit G

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit E

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

4dl0__assembly_1__model_1

4dl0__assembly_1__model_1 | I(q)

4dl0__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase

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

V-type proton ATPase subunit C

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 G

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 E

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

4dl0__assembly_1__model_1

4dl0__assembly_1__model_1 | I(q)

4dl0__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)