SAXSdb — 5tj5

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

V-type proton ATPase subunit a

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit f × 1 V-type proton ATPase subunit d × 1 （P32366）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPH1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 251–680； UniProt 400–829

;V-type proton ATPase subunit c'' ;

OrganismNot specified

UniProt P23968

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	V-type proton ATPase subunit a × 1 （P32563） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit f × 1 V-type proton ATPase subunit d × 1 （P32366）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATO_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–213； UniProt 1–213

;V-type proton ATPase subunit c' ;

OrganismNot specified

UniProt P32842

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	V-type proton ATPase subunit a × 1 （P32563） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit f × 1 V-type proton ATPase subunit d × 1 （P32366）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATL2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–147； UniProt 17–163

V-type proton ATPase subunit c

OrganismNot specified

UniProt P25515

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	V-type proton ATPase subunit a × 1 （P32563） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit f × 1 V-type proton ATPase subunit d × 1 （P32366）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATL1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–150； UniProt 9–158 Author chain F； PDBConstruct 1–150； UniProt 9–158 Author chain G； PDBConstruct 1–150； UniProt 9–158 Author chain H； PDBConstruct 1–150； UniProt 9–158 Author chain I； PDBConstruct 1–150； UniProt 9–158 Author chain J； PDBConstruct 1–150； UniProt 9–158 Author chain M； PDBConstruct 1–150； UniProt 9–158 Author chain N； PDBConstruct 1–150； UniProt 9–158

V-type proton ATPase subunit e

OrganismNot specified

UniProt Q3E7B6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	V-type proton ATPase subunit a × 1 （P32563） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit f × 1 V-type proton ATPase subunit d × 1 （P32366）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VA0E_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–57； UniProt 5–61

V-type proton ATPase subunit d

OrganismNot specified

UniProt P32366

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	V-type proton ATPase subunit a × 1 （P32563） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit f × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VA0D_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain P； PDBConstruct 1–152； UniProt 4–155 Author chain P； PDBConstruct 173–198； UniProt 176–201 Author chain P； PDBConstruct 240–297； UniProt 284–341

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	5tj5
Deposition date deposition_date	2016-10-03
Structure title title	Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase
Keywords keywords	Rotary ATPase, Vacuolar-type ATPase, Electron Cryomicroscopy, Vo region, Membrane protein, MOTOR PROTEIN; MOTOR 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.

5tj5__assembly_1__model_1

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

Download this curve (.dat)

5tj5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tj5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.03 Å
Rg (electron density)	40.81 Å
Total Rg	41.07 Å
Atom count	14976
Residues	2467
Excluded volume	261610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tj5__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 (7)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase subunit a
Molecular weight formula_weight	70068.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14976

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAQYREINAGLPTIVTFPFMFAIMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEV

Entity 2 Entity 2 polymer

Description description	;V-type proton ATPase subunit c'' ;
Molecular weight formula_weight	22610.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSALFVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Entity 3 Entity 3 polymer

Description description	;V-type proton ATPase subunit c' ;
Molecular weight formula_weight	15195.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

FFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGS

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit c
Molecular weight formula_weight	15218.1 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

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

APFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDV

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit e
Molecular weight formula_weight	6476.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

YTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLVA

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase subunit f
Molecular weight formula_weight	4613.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit d
Molecular weight formula_weight	32854.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

VYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDXXXXXXXXXXXXXXXXXXXXNIEIIRNKLYKAYLEDFYNFVTEEIPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLEDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNY

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5tj5E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	610 — lithium bound rotor ring of v- atpase

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Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	462842

Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase

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

V-type proton ATPase subunit a

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 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 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 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 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5tj5__assembly_1__model_1

5tj5__assembly_1__model_1 | I(q)

5tj5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)